The low head pump is widely used in many important water conservation projects for drainage and irrigation purposes. A new type of low head pump, the bidirectional shaft tubular pump, consists of an S-shaped impeller, a straight-guide vane, an inlet section, and an outlet section. As known from the practical project, the distance between the impeller and guide vane of the bidirectional shaft tubular pump greatly affects a pump’s performance; however, because of its unique impeller and guide vane structure, the distance between the two cannot be easily determined by general empirical formulas. Therefore, in this research, three-dimensional unsteady numerical simulations were performed for six guide vane positions under positive and negative rotation conditions, and the accuracy of the results was experimentally verified. The entropy production method based on numerical results was used to evaluate the effect of the distance on the internal flow-loss distribution and overall power loss, and as a result, a better understanding of the hydraulic loss mechanisms was obtained. The results show that the distance between the impeller and guide vane of a bidirectional shaft tubular pump can affect the pump’s efficiency under a positive rotation condition, and turbulence dissipation is the dominant loss. This study can provide theoretical guidance to improve the hydraulic efficiency of low head pumps.