A spacecraft universal interface controller comprises a bus HOST interface processing unit, a UART interface processing unit, a TDM arbitration processing unit, an instruction parse processing unit, a time sequence parallel interface processing unit, non-time-sequence parallel interface processing unit, a serial data output interface processing unit, a serial data input interface processing unit, a serial data collection interface processing unit and a remote measuring status framing processing unit.The universal controller achieves protocol processing and time sequence control of a time sequence parallel interface, a non-time-sequence parallel interface, a serial data output interface, a serial data input interface and a serial data collection interface through a replaceable processer, data interaction and protocol processing among the interfaces such as a satellite-borne bus and a UARAT interface, the bus system structure of a traditional spacecraft comprehensive electronic computer, information interaction between the processor and the interfaces is simplified, and the overall performance of a spacecraft comprehensive electronic system.