The world is replete with complex and interactive relationships (e.g., between causes and effects; between categories and their properties), and effective thinkers must learn to represent and reason about this complexity. I introduce a "structural thinking" framework for describing some aspects of reasoning about complex systems where an organized larger whole (a structure) imposes constraints on properties of its elements. In a series of studies with children and adults, I examine how people acknowledge instability of causal and categorical relationships with respect to background variables, and recognize confounds between category membership and social positions. Structural thinking emerges as a distinct, early-developing mode of thought with a unique cognitive and behavioral profile which distinguishes it from other types of reasoning focused either on internal or external but non-structural factors. For example, structural thinking promotes an expectation that properties of social kinds are mutable rather than stable; fosters rectification of inequality in resource allocation decisions; and supports formal explanations (i.e., “category member has property P due to category membership C”), generic claims (“Cs have P”), and some forms of generalization. This evidence highlights important connections between causal and categorical representations, and invites us to rethink dominant theories of categorical representations and generic language.