The invention relates to a system and a method for testing a secondary circuit on site in an intelligent substation. The system comprises an overhauling and testing center and at least one test terminal which is in communication connection with the overhauling and testing center, and is characterized in that the test terminal is close to equipment to be tested, and used for sending analog or digital signals to the equipment to be tested and acquiring outlet node information of the equipment to be tested; the overhauling and testing center is used for configuring test data of each test terminal, sending the test data to each test terminal and judging the correctness of the equipment to be tested according to test feedback data of the equipment to be tested and MMS (Manufacturing Message Specification) information. The test system can realize that the test personnel perform dosage on equipment to be tested, which are dispersively arranged in a switch factory, in a control room of the substation, whether protection response is correct or not is checked at a protection device end, and the correctness of station control level information on an MMS message monitoring device is analyzed, thereby forming closed-loop testing, and realizing a complete test for the secondary circuit of the intelligent substation. The system and the method provided by the invention improve the test efficiency and reduce the test cost.