In a subchannel analysis, the assumptions of the physical models may be invalid when three-dimensional (3-D) effects play an important role because a large-scale model cannot consider a small-scale physical process. However, in a pressurized water reactor (PWR), the flow process has a high 3-D effect due to the effect of complex structures, such as dimple, spring, and mixing vane. A computational fluid dynamics (CFD) analysis can give more detailed physical information. So, the modeling assumptions of the subchannel analysis codes were analyzed using data from CFD analysis, and some issues were found: The spatial acceleration of the cross-flow rate and the viscous force from fluid to fluid should not be neglected; the lateral pressure gradient not only is a driving force but also can be a resistance at some vertical range; the traditional “resistant force term” has the same direction with the cross flow at some vertical ranges. To improve the subchannel code, one physical term considering both the driving and the resistance effect is suggested to be added in the traditional transverse momentum equation. The solution for this new term and the method using spatial acceleration of the cross flow were also provided.