The knowledge of food web spatial heterogeneity is important for ecologists and lake managers to understand ecosystem complexity and lake management. Lake Taihu, a large shallow eutrophic lake in China, has two distinct zones: algae- and macrophyte-dominated. In this study, we assessed the spatial heterogeneity of food webs in the two lake zones using stable isotope analysis and isotope mixing model. The basal sources and consumers showed significant differences in delta C-13 and delta N-15 ratios between the two lake zones, except for the filter-feeding fishes. Overall, more delta C-13-depleted and delta N-15-enriched ratios were found in the algae- than the macrophyte-dominated zones for basal sources and consumers. Although the consumers in the algae-dominant zone had higher average delta N-15 values, the food web of the macrophyte-dominated zone had longer food chain length and more diverse trophic linkages. These spatial differences may have resulted from resource availability and environmental stress of Lake Taihu ecosystem. Factors associated with spatial trophic heterogeneity should be considered for the management and restoration of this shallow eutrophic lake.