Titanium dioxide nanoparticles (TiO₂ NPs) are widely used as nano-agrochemicals. In this study we investigated the influence of soil heterogeneity on bacterial communities exposed to TiO₂ NPs over time. Clay and sandy soils with low- and high-organic matter contents were exposed to environmentally relevant concentration of TiO₂ NPs (1 mg/kg) and soil bacterial communities were sampled after short-term (15 days) and long-term exposure (60 days). After short-term TiO₂ NPs exposure, significant effects regarding the enzyme activity, bacterial community structure and composition, and community functioning were observed in the clay soils with high organic matter (clay-HOM) but not in other soil groups. Response alterations were observed to taxa belonging to Acidobacteria and Verrucomicrobia, and functional pathways related to carbohydrates degradation. These results indicated that soil heterogeneity play more important roles in shaping the bacterial community in soil with low clay fraction and less organic matter, while TiO₂ NPs selection was the main driver in inducing the compositional and functional impacts on the soil bacterial community in the presence of clay soil with high organic matter content. As exposure time increased, the bacterial community recovered after a long-term exposure of 60 days, suggesting that the bacterial evolution and adaptation could overcome the TiO₂ NPs selection after long-term exposure. Our results highlighted the importance of soil heterogeneity including clay fraction and organic matter and exposure duration in assessing the impact of nanoparticle on soil bacterial activity, community and function. By comprehensively evaluating the risks of nanoparticles on soil ecosystem and explicitly and explicitly include spatial and temporal variations, the benefit of nano-agrochemical products has the potential to be promoted in future applications.