A method and system for flexible deployment and easy CPLD management of a backplane are provided. An EEPROM module is added on a backplane; a connection configuration mode of a hard disk backplane and a motherboard controller is stored in the EEPROM module; and a CPLD reads connection relationship information from the EEPROM by means of I2C so as to perform a lighting function and other similar control functions. In addition, by means of adding a connection of a BMC management module on a motherboard to the EEPROM module, when the configuration is changed, a BMC directly upgrades the stored information in the EEPROM module by means of an I2C bus without needing to disassemble a machine. In the method and system, only two pins of the CPLD need to be occupied, without needing to consider that more CPLD pins are required for more complex configurations.