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Impacts of the spatial structure of weather generators on hydrological modeling have been largely qualitatively discussed; however, their links have been rarely quantified. The precipitation occurrence and amount were respectively generated with Markov chain and the mixed exponential distribution for single sites, and then the procedures were extended to multi-site simulation according to Wilks (1998). In the multi-site model, precipitation amounts were respectively generated with untapered or tapered mixed exponential scale parameters. The generated precipitation series were used as inputs of Soil and Water Assessment Tool (SWAT) to interpret the links between the spatial structure of weather generators and hydrological modeling. The single-site and multi-site model using untapered scale parameters gave similar averages for monthly and annual streamflow; however, the untapered multi-site model was superior to simulating hydrological variability. The single-site model underestimated the maxima and variances while overestimated the minima of streamflow; therefore, the use of single-site models for hydrological variability simulation should be cautious. The multi-site model using tapered scale parameters greatly overestimated the averages, extremes, and variances of streamflow. The Wilks model for multi-site precipitation simulation using tapered scale parameters is not appropriate for hydrological modeling, and the untapered version is thus recommended. Overall, the spatial structure of weather generators has significant impacts on hydrological modeling, especially for hydrological variability simulation; therefore, the links between them should be paid great attentions.