A connector cover assembling system includes an arrangement apparatus, which aligns covers and includes a transporting channel for transporting the covers to a frame that supports the covers and associated connector bodies. A cover driving member transports the covers one by one from the frame to a separating mechanism, which further transports the cover to a location above a clamping mechanism for being clamped by the clamping mechanism. A lifting mechanism drives an inserting mechanism and the clamping mechanism to the separating mechanism. The clamping mechanism clamps the covers from the separating mechanism. The inserting mechanism drives the clamping mechanism to transport and assemble the cover to the connector body. A holding mechanism holds the connector body during the assembling operation. The control unit coordinates operations of the above-mentioned components. Therefore, manufacturing efficiency of electrical connector can be improved and manufacturing costs reduced.