The invention discloses a comprehensive intelligent time frequency testing system and a testing method. The system comprises a GPS (global positioning system)/Big Dipper antenna receiver, a management machine, a time frequency standard source and time standard pulse testing equipment, standard frequency testing equipment, IRIG (inter range instrumentation group) -B timing code testing equipment, a NTP/SNTP (network time protocol/simple network time protocol) message testing equipment and a PTP (precision time synchronization protocol) message testing equipment. The management machine is provided with a database and is used for running a testing and analyzing management program. The time frequency standard source is used for connecting the management machine through a communication link to realize program control. An intelligent time frequency signal switcher is provided, and the program control of the management machine is realized through the testing and analyzing management program; moreover, the switch of the program control is carried out by the intelligent time frequency signal switcher for carrying out a comprehensive intelligent time frequency test. The intelligent comprehensive test to the tested time synchronous equipment can be effectively and easily carried out with no need of manual intervention, so that the intelligentization, the standardization and the systematization levels of the tests of the complicated service function and performace of the time synchronous equipment are practically improved, the test performance is more correct, the testing efficiency is higher, and the testing time is greatly shortened.