On the basis of summarizing and elaborating the similarities, differences, and applicability of one-dimensional unsteady convection-heat transfer model theory, the hyporheic zone of the Walker River Basin in the United States was chosen as a case study, of which the VFLUX 2 program was carried out to calculate and compare the differences between different one-dimensional analytical models for quantifying the vertical hyporheic exchange fluxes in the hyporheic zone. The optimal analytical model for solving the vertical hyporheic exchange flux was verified and determined, and the spatial-temporal variation of the hyporheic exchange flux at different depths in the hyporheic zone was investigated. The advantages and disadvantages of the analytical model and the focus of future work using the heat tracer method were discussed from the perspective of theoretical analysis. The results show that the amplitude method can reasonably reflect the interaction between surface water and groundwater in the hyporheic zone compared with the phase and amplitude-phase combination methods, which is an ideal model to quantify the vertical hyporheic exchange flux. The hyporheic exchange flux at different depths of the hyporheic zone is significantly different. The hyporheic exchange is frequent in the shallow, and the exchange effect is suppressed with the depth increase. In the future, a more reasonable and suitable numerical model for quantifying the hyporheic exchange flux using the heat tracer method for complex engineering conditions should be considered.