The storage cells of conventional submarines are usually charged up by in the snorkeling state, when the diesel engines that charge the storage cells work underwater. The reverse flow of sea water into the diesel engine from the exhaust pipelines can be avoided effectively by using a water-collecting box (WCB), which has other functions as well. In this paper, a three-dimensional model of WCB was established and based on which the flow and temperature fields were studied by computational fluid dynamics (CFD) computations. From the comparison of distribution on interior fields for four different structural WCBs, an optimized scheme of enhancing the cooling effect and not raising the exhausting resistance was probed. The results show that the temperature drop of exhaust gas after washing the WCB IV (WCB with truncated tubes) is 40 percent higher than that of the WCB I, and the pressure drop has a low of 3 percent as well. The comprehensive characteristics of WCB IV are foremost between the four WCBs.