Two cylinder heads are disposed side by side. Upper side intake valve holes of one of the cylinder heads and upper side exhaust valve holes of the other of the cylinder heads are simultaneously machined by a multi-spindle head integrally including intake side tools and exhaust side tools. After moving the one of the cylinder heads upward by a pitch of the intake valves and moving the other of the cylinder heads upward by a pitch of the exhaust valves, remaining intake valve holes of the one of the cylinder heads and remaining exhaust valve holes of the other of the cylinder heads are simultaneously machined.