The invention provides an online upgrading method for a multi-module system and a rotary guiding system. The online upgrading method comprises the steps that the multi-module system is connected withan upper computer through a single bus; The upper computer automatically sends a software upgrading instruction to each module in the multi-module system; Each module receives the software upgrading instruction and modifies the corresponding storage value in the EEPROM memory; the multi-module system is powered off and the multi-module system is powered on again; Each module runs the respective BootLoader program and reads the storage value in the corresponding EEPROM memory, and for the module of the to-be-upgraded program, the BootLoader program receives the upgrading program data and writesthe upgrading program data into the corresponding FLASH memory; And for other modules which do not need to be upgraded, the storage value in the EEPROM is erased and the module upgrading program of the program to be upgraded is waited for. By applying the technical scheme, the technical problems that in the prior art, a software upgrading method is inconvenient to operate and low in efficiency, and the sealing performance of an instrument cannot be guaranteed are solved.