The invention discloses a server fan control method and system based on configuration of different types of board cards and belongs to the technical field of server cooling technologies. According to the server fan control method and system based on configuration of different types of the board cards, fan control programs for configuration of different types of the board cards are integrated in a BMC, and the different fan control programs correspond to different control temperature points and fan rotation speeds; and communication connection of the BMC and a BIOS is built, related information of the board cards in the BIOS is obtained by the BMC, and the different fan control programs are automatically called according to the related information of the board cards collected by the BMC, so that different cooling control manners are enabled, and the control over the working state of a fan is completed. According to the server fan control method and system based on the configuration of different types of the board cards, the rotation speed of the fan can be optimized, the cooling performance of a server is guaranteed, the noise of the server can be lowered effectively, and the server fan control method and system have the good application and popularization value.