Based on the energy loss analysis of the sliding pair between plunger and cylinder, a mathematical model of overall efficiency loss was established. Based on the principle of minimum overall efficiency loss, a calculation method of minimum length retained in cylinder was proposed. In order to ensure the plunger was not stuck during the relative movement because of friction self locking, a strength check method of the sliding pair was proposed to validate the rationality of the calculated minimum length. And according to the strength check method, the minimum length and corresponding plunger geometry length were calculated. Under the principle of minimum loss of total efficiency, the optimum clearance of sliding pair was calculated by the strength check method. A case analyzed and verified the correctness of the calculation method, the calculated minimum length is 35mm or 40mm for the plunger pump used on an engineering machinery, the corresponding optimal clearance is 0.012mm or 0.0127mm, and the theoretical calculated overall efficiency loss is 0.3%.