The interacting components of a complex system form a network, which is a collection of discrete objects and relationships between them, usually depicted as a graph of vertices connected by edges. Networks can describe the relationships between individuals within an organization, between logic gates in a circuit, between genes in gene regulatory networks, or between any other set of related entities.

Networks often describe the sources of complexity in complex systems. Studying complex systems as networks, therefore, enables many useful applications of graph theory and network science. Many complex systems, for example, are also complex networks, which have properties such as phase transitions and power-law degree distributions that readily lend themselves to emergent or chaotic behavior. The fact that the number of edges in a complete graph grows quadratically in the number of vertices sheds additional light on the source of complexity in large networks: as a network grows, the number of relationships between entities quickly dwarfs the number of entities in the network.

Another common feature of complex systems is the presence of emergent behaviors and properties: these are traits of a system that are not apparent from its components in isolation but which result from the interactions, dependencies, or relationships they form when placed together in a system. Emergence broadly describes the appearance of such behaviors and properties, and has applications to systems studied in both the social and physical sciences. While emergence is often used to refer only to the appearance of unplanned organized behavior in a complex system, emergence can also refer to the breakdown of an organization; it describes any phenomena which are difficult or even impossible to predict from the smaller entities that make up the system.

For a system to exhibit complexity means that the systems' behaviors cannot be easily inferred from its properties. Any modeling approach that ignores such difficulties or characterizes them as noise will necessarily produce models that are neither accurate nor useful. As yet no fully general theory of complex systems has emerged for addressing these problems, so researchers must solve them in domain-specific contexts. Researchers in complex systems address these problems by viewing the chief task of modeling to be capturing, rather than reducing, the complexity of their respective systems of interest.

While no generally accepted exact definition of complexity exists yet, there are many archetypal examples of complexity. Systems can be complex if, for instance, they have chaotic behavior (behavior that exhibits extreme sensitivity to initial conditions, among other properties), or if they have emergent properties (properties that are not apparent from their components in isolation but which result from the relationships and dependencies they form when placed together in a system), or if they are computationally intractable to model (if they depend on a number of parameters that grows too rapidly with respect to the size of the system).

Complex systems often have nonlinear behavior, meaning they may respond in different ways to the same input depending on their state or context. In mathematics and physics, nonlinearity describes systems in which a change in the size of the input does not produce a proportional change in the size of the output. For a given change in input, such systems may yield significantly greater than or less than proportional changes in output, or even no output at all, depending on the current state of the system or its parameter values.

Of particular interest to complex systems are nonlinear dynamical systems, which are systems of differential equations that have one or more nonlinear terms. Some nonlinear dynamical systems, such as the Lorenz system, can produce a mathematical phenomenon known as chaos. Chaos, as it applies to complex systems, refers to the sensitive dependence on initial conditions, or "butterfly effect", that a complex system can exhibit. In such a system, small changes to initial conditions can lead to dramatically different outcomes.