The invention discloses a method of data flow programming oriented to CPU/GPU heterogeneous clusters. The method comprises the steps of utilizing a data flow program to obtain a SDF diagram, conducting hierarchical secondary task division and scheduling on the SDF diagram, setting a stage number for each task unit to obtain the execution order of the task units; utilizing a CPU kernel or GPU mapping from the task unit to heterogeneous cluster nodes in the SDF diagram and a heterogeneous cluster multitask data communication model to obtain data communications between the task units, and obtaining target codes according to the execution order of the task units and the data communications between the task units. According to the method and system of data flow programming oriented to CPU/GPU heterogeneous clusters, the data communications are optimized with the parallelization of the data flow programs, and the overall execution performance of the programs is improved.