The invention discloses a CAN bus structure for a full automatic medical detecting instrument. The CAN bus structure comprises a CAN bus system connected with master control, wherein CAN transceiversand CAN controllers are connected with a CAN bus; the CAN controllers are connected with sub-module controllers; the sub-module controllers are connected with sub-module performance mechanisms and multidigit dip switches. According to the CAN bus structure, the master controller of the medical detecting instruction and auxiliary sample injection module, detection module, signal conversion module,display and print module and data storage module at the periphery of the instrument are mounted on the CAN bus and the modules are relatively independent, so the development efficiency can be improved, the universality is relatively high, and certain module can be added or deleted relatively conveniently. A control algorithm is relatively mature, the intelligent level of the medical detecting instrument can be improved, and certain fault self-checking capability is achieved. The controllers are connected with the sub-modules in a CAN bus mode, so the stability and the anti-interference performance of the system are improved.