The invention discloses a control system and control method of onsite error checking of a heavy current transformer. Most of control systems used for onsite error checking of heavy current transformers in the prior art are tedious, poor in safety and low in working efficiency. In the provided control system, a current transformer onsite checking system and a test environment monitoring system are connected with an integrated operation system. The integrated operation system comprises an integrated operation bench and a human-machine interaction big screen embedded in the integrated operation bench. The control method comprises steps that current tests are selected and an electronic power supply or an electrician power supply is selected to be started on the integrated operation bench according to test requirement; the integrated operation system automatically calculates primary parameters of a checking loop and required compensation capacity, and controls a switching capacitive compensation device to carry out compensation; and the integrated operation system begins to automatic rising current checking and generates a test report. The provided control system is advantaged by high working efficiency, safety, stability, and high checking accuracy.