The filling and emptying system selection is the key issues of navigation lock design. For the filling and emptying system，type selection mainly considers the deviation caused by the design head H and the water filling emptying time T. In this paper，according to the energy dissipation mechanism of the filling and emptying system，combined with the influences of water head，filling and emptying time，chamber dimension and initial water depth on the basis of the traditional discrimination index m，two dimensionless energy per unit area indexes mL and mc are introduced. The decision indexes of 123 navigation locks with different characters are counted，then the relationship between the indexes and the filling and emptying system is established using gray system theory. Finally，using the filling and emptying system selection model，the filling and emptying system of 13 typical ship locks are calculated and compared with the industry codes. The results show that this method quantifies the filling and emptying system selection process；the filling and emptying system selected by this method has high accuracy and good practical value.