In this paper, we consider the synchronization of a class of nonlinear network flow systems. Motivated by air distribution problem in air conditioning and mechanical ventilation (ACMV) systems, we propose a class of coupled nonlinear multi‐agent systems that can model a wide class of network flow systems, including air flow in ACMV systems, water flow in irrigation systems, traffic flow in transportation systems, and so on. Then we consider the synchronization problem for the class of nonlinear multi‐agent systems and propose cooperative controllers for the system. Based on graph theory, we derive conditions on the initial values of the state and the control input such that synchronization can be achieved. An application to air ventilation is provided to demonstrate the effectiveness of the cooperative controllers. Copyright © 2015 John Wiley & Sons, Ltd.