The invention discloses a system and method for inspecting a small-signal output type unconventional mutual inductor, which belong to the field of measurement. The system comprises a small-signal output type unconventional current mutual inductor and an output terminal box thereof, wherein the small-signal output type unconventional current mutual inductor is provided with a control terminal, a current output terminal and a signal acquisition terminal; the current output terminal is connected with a primary loop of the small-signal output type unconventional current mutual inductor by a cable; the signal acquisition terminal is connected with an output interface of the output terminal box of the small-signal output type unconventional current mutual inductor by a shielded cable; a control terminal device, a current output terminal device and a signal acquisition terminal device are connected in a wireless mode so as to form a system; the control terminal carries out operating parameter setting and synchronization implementation on the current output terminal and the signal acquisition terminal; the current output terminal device outputs a current so as to simulate the situation of the primary loop in the process of actual running; and the signal acquisition terminal carries out acquisition and analysis on the data of the small-signal output type unconventional current mutual inductor, then sends the data to the control terminal so as to carry out data analysis, and then a test result is obtained. The system and method disclosed by the invention can be widely used in the on-site inspection field of unconventional mutual inductors.