A system of performing boundary scan test on pin through test point and a method thereof are disclosed. When an under-test pin of a target connector is determined to be unable to perform a boundary scan test, a test point connected to and closest to the under-test pin is searched, a test signal is transmitted to a target connector, a result signal from the target connector in response to the test signal is received, an expected result and the result signal are compared to generate a test result, so that a boundary scan function can be applied to test a connector of a computer product, to achieve the technical effect of providing a better test range and a better test coverage to improve test efficiency and reduce test cost, compared to conventional boundary scan test.