A control system is provided with a piston TDC (top dead center) position variable mechanism and a valve operational characteristics variable mechanism. An actual distance between the valve and the piston of closest approach is calculated based on the actual operation states of these mechanisms. In addition, a limit distance of closest approach necessary to avoid interference between the valve and the piston is set, and, the piston TDC position variable mechanism and the valve operational characteristics variable mechanism are controlled to be driven to increase the actual distance.