The invention discloses a multi-FPGA logic loading method in an embedded system. The method comprises: firstly, performing power-on reset on a target device and loading an FPGA logic; secondly, judging whether the current functional configurations of the target device are matched with functional configurations supported by the currently loaded FPGA logic, if yes, ending up loading the FPGA logic,if not, shifting to a third step; and thirdly, loading the FPGA logic corresponding to the current functional configurations of the target device. The method decomposes different functional configurations and compiles a plurality of FPGA logics according to various functions which are required to be realized by the target device, so as to reduce the difficulty coefficient of FPGA logic development, achieves self-adaptive loading of the FPGA logics by selecting and judging the various FPGA logics, realizes various functional configurations of the target device, and simultaneously reduces the cost.