The invention relates to a control mechanism for preventing generator set inlet ball valve work seal from automatically exiting and a using method thereof. The control mechanism comprises a main operation valve connected with a pressure stop valve and an overhaul seal locking valve; the main operation valve is connected with a servomotor device and a closing valve, the closing valve is connected with an opening valve sequentially through an accident closing valve and a mechanical signal overspeed valve, the opening valve is connected with the overhaul seal locking valve through a work seal locking valve, a horizontal press control valve connected with a bypass needle valve is connected between the work seal locking valve and the overhaul seal locking valve in parallel, the bypass needle valve is arranged on a bypass pipeline, and an overhaul needle valve is arranged on the bypass pipeline and is connected with an open control valve; inlet ball valve overall seal is connected with the work seal control valve, the work seal is connected with an overall seal control valve, and the work seal control valve and the overall seal control valve are connected with the work overall seal locking valve controlled by the servomotor device. The control mechanism can ensure safe and reliable operation of a generator set and an inlet ball valve system.