All cell components exhibit intracellular noise due to random births and deaths of individual molecules, and extracellular noise due to environment perturbations. In particular, gene regulation is an inherently noisy process with transcriptional control, alternative splicing, translation, diffusion and chemical modification reactions, which all involve stochastic fluctuations. Such stochastic noises may not only affect the dynamics of the entire system but may also be exploited by living organisms to actively facilitate certain functions, such as cooperative behavior and communication. Results: We have provided a general model and an analytic tool to examine the cooperative behavior of a multi-cell system with both intracellular and extracellular stochastic fluctuations. A multi-cell system with a synthetic gene network is adopted to demonstrate the effects of noises and coupling on collective dynamics. These results establish not only a theoretical foundation but also a quantitative basis for understanding essential roles of noises on cooperative dynamics, such as synchronization and communication among cells.