Let’s deconstruct this often made claim that systems thinking (ST) stands in contrast to (in this case on opposite ends of a continuum from) reductionism. This claim appears reasonable at first, and it is one made my many of the founding fathers of systems thinking as well as contemporary systems thinkers. But there are some dangers, mostly having to do with misleading people new to the field toward misunderstanding what it means to be a systems thinker.

First, if reductionism (breaking things down into their constituent parts) is on one side of a continuum, then holism (seeing things in the context of their whole) is on the other. If reductionism is the opposite of ST, then ST and holism are synonymous. Here lies the problem…

No matter how holistic one gets, there is always a larger whole to act as context, and one is therefore always surgically removing the whole under consideration from the whole it is a part of, which is one of the chief criticisms with reductionism. So being a pure holist who does not reduce or being a pure reductionist who is not holistic is absurd and it is a false dichotomy. We need to do both just to begin thinking about anything.
Therefore, to break things down into parts (reductionism) is an act of systems thinking as much as seeing things in the context of their whole. A healthy part-whole balance is a necessary aspect of systems thinking. There’s an old saying that there are two kinds of scientists: splitters and lumpers. Systems thinking then is the act of not accepting this duality and of being a "splumper."

Of course, this creates another problem. When we “break” things down into their structural parts, we are “breaking” the dynamical relationships, so we must therefore take extra caution to identify the broken relationships and think of them as the dynamical parts of the whole (or we may end up with unexplainable phenomena that we must label emergence).
Of course, now we have another problem: that even our most holistic thinking cannot be infinite and complete. Even holistic thinking must draw a boundary somewhere. At the very least between what we consider and what we do not. At that moment a distinction forms between what we decided to consider and what we decided not to consider. This boundary is a distinction where we identify some thing(s) as being inside the scope of our observation and some other things as being outside the scope.

This in turn causes yet another problem which is that the choice of a boundary is a subjective one, requiring perspective, so we must consider that these distinctions we make for the whole (and each subsequent distinction we make of the parts) is perspectival. Change our perspective and the distinctions we make change, too.

And this makes us realize why we must challenge the "parts are more than the whole" trope (W=P versus W<P) because these concepts become interconnected.

Because, even if you only wanted to understand the whole (holism), you would be forced to also understand the parts. Because the parts (which include the relationships) is where the whole is born.

The repudiation of reductionism was popularized in the ST space (historically speaking) by Bertalanffy. And, he was somewhat "right" (or at least it was necessary) in focusing on holism over reductionism. The reason he did was because he was fighting a scientific establishment that was woefully imbalanced toward reductionism. Ergo, he emphasized holism. Unfortunately, this emphasis has taken hold and become a trope. A holistic emphasis was never the intended long-term goal, it was a short-term strategy to fight reductionism ad absurdum (which is not the same as reductionism). The long term goal is a necessary balance. The argument between holism and reductionism is akin to the debate between nature and nurture. They are both so integrally intertwined that speaking about one without considering the other is hard to do.

One need only to look at the great discoveries that we would consider "systemic in nature" to see that the scientific process that those discoveries took required a balance of reductionism and holism (focus on the parts and the whole and deep relationships between them).

This is just one of the "Sacred Cows" of Systems Thinking. Click the link to see all all sacred cows and their scientifically valid replacements.

For a much more extensive introduction to these ideas see the new book, Systems Thinking Made Simple: New Hope for Solving Wicked Problems.