The invention provides a method for removing an on-track latch fault of a spread spectrum responder of a spacecraft. The method includes a first step of establishing a spread spectrum responder state relational table which is used for fixedly storing the corresponding relation between a current state of the spread spectrum responder and a next expectation state of the spread spectrum responder, and a second step of enabling a central processing unit (CPU) of a satellite data management subsystem to obtain the state of the spread spectrum responder during each acquisition cycle, and judging whether the acquired state of the spread spectrum responder accords with the corresponding expectation state recorded in the spread spectrum responder state relational table during the acquisition cycle through searching to the spread spectrum responder state relational table and judging whether the spread spectrum responder works properly. When continuous working abnormal states of the spread spectrum responder last the fixed quantity of state cycles, the CPU can judge that the on-track latch fault happens to the spread spectrum responder. At the moment, the CPU sends a spread spectrum responder power-off instruction and then resends a spread spectrum responder power-on instruction after ensuring that the spread spectrum responder is powered off in a delayed time interval. The one-time removal work of the latch fault of the spread spectrum responder is completed.