The invention discloses a controller and testing method of boundary scanning, said controller includes PC unit, USB interface unit, two-end memory unit, control and transforming unit; said PC unit can set test, generate test vector, send and receive test data, analyze test data, store test result and USB drive of controller; said USB interface unit realizes communication between boundary scanning test controller and computer; said two-end memory unit realizes memory of test vector and stores test response; said control and transforming unit generates boundary scanning test clock to realize transforming test data to JTAC signal, and realizes reading and writing of data from two-end memory unit. The invention adopts USB interface, memory of two-end memory unit and FPGA design, plug and play, data transmission and boundary scanning test can be preceded at the same time, test speed is increased.