In order to control large-scale accelerators efficiently, a control system with a virtual accelerator model was constructed. The virtual accelerator (VA) is an on-line beam simulator provided with a beam monitor scheme. The VA is based upon the Experimental Physics and Industrial Control System (EPICS) and is configured under the EPICS input/output controller (IOC) in parallel with a real accelerator (RA). Thus, the machine operator can access the parameters of the RA through the channel access client and then feed them to the VA, and vice versa. Such a control scheme facilitates developments of the commissioning tools, feasibility study of the proposed accelerator parameters and examination of the measured accelerator data. This paper describes the beam commissioning results and activities by using the VA at the J-PARC 3-GeV rapid-cycling synchrotron (RCS).