The invention discloses a multiple-shaft drill bit machine tool for processing a threaded bottom hole in the side surface of a crank case and a processing method thereof. The multiple-shaft drill bit machine tool comprises a workpiece mounting table and a multiple-shaft drill head, wherein the crank case is fixed on the workpiece mounting table, and bottom hole drilling is performed to a thread of the side surface of the crank case through the multiple-shaft drill head. The invention provides a production machine tool with a better effect, the defects that position accuracy of drilling the thread of the side surface of a gear case in the conventional production is difficult to ensure, the processing efficiency is low, the labor intensity is large and the like are overcome, the drilling position accuracy is improved and stabilized, the frequency of drilling is reduced, and meanwhile, the multiple-shaft drill bit machine tool can displace manual operation through a numerical control mode, improves the machine productivity, lowers the labor intensity, remarkably improves the whole production efficiency, saves the total cost, and can efficiently propel the development of the prior art.