A software and hardware collaborative compilation processing method and system. The system comprises an environment configurator, a command parser, a code filler, a scheduler and a heterogeneous target system, wherein the code filler is configured for obtaining the source program path of a user, reading source codes and identifying the heterogeneous target system according to a macro definition, complementing the codes related to the heterogeneous target system, carrying out primary filling and secondary filling on the source codes; the scheduler is configured for realizing compilation scheduling and execution scheduling functions respectively; the heterogeneous target system is configured for compiling and processing user modal data, and comprises at least two heterogeneous target subsystems; each target subsystem comprises a target-related middle-end compiler, a back-end compiler and a target-related running environment.