The invention relates to a method and system for testing an error of a correction field of a peer-to-peer transparent clock, and a clock tester. The system comprises the clock tester connected with the peer-to-peer transparent clock to be tested, wherein the clock tester is provided with a master clock port and a slave clock port; the master clock port and the slave clock port are connected with two ports of the peer-to-peer transparent clock to be tested respectively through two optical fibers; the master clock port is used for sending a synchronous message; the slave clock port is used for receiving the synchronous message; and the clock tester is also connected with a background computer for analyzing information acquired by the clock tester. Based on the clock tester which supports an IEEE1588-2008 protocol, the frequency modulation effectiveness of the peer-to-peer transparent clock and the correctness of the correction field calculated by the peer-to-peer transparent clock are analyzed through performing linear regression analysis and distributed analysis on a plurality of groups of test data by the background computer with statistical analysis software.