The invention discloses a CNN acceleration method and system based on OPU, and relates to the field of CNN acceleration methods based on FPGA. The method includes that an OPU instruction set is defined; the compiler converts the CNN definition files of different target networks, selects an optimal accelerator to configure mapping according to the defined OPU instruction set, and generates instructions of different target networks to complete mapping; the OPU reads the compiled instruction, operates the instruction according to a parallel computing mode defined by the OPU instruction set, and completes acceleration of different target networks. According to the method, the instruction type is defined, the instruction granularity is set, network recombination optimization is carried out, a mapping mode for guaranteeing the maximum throughput is obtained by searching a solution space, and hardware adopts a parallel computing mode; the problem that an existing FPGA acceleration work aims at generating specific independent accelerators for different CNNs is solved, and the effects that the FPGA accelerator is not reconstructed, and acceleration of different network configurations is rapidly achieved through instructions are achieved.