The toxic factor (TF) is a key parameter commonly used to evaluate the potential ecological risk index (RI) of heavy metals. It is still unclear whether it is suitable to assess the risk on soil microorganisms by heavy metals. Here, we established soil microcosms with a gradient of RI levels (100, 200 and 400) by different combinations of lead (Pb) and cadmium (Cd) concentrations based on the TF values of 5 and 30 for Pb and Cd, respectively. Biolog-ECO microplate and high-throughput sequencing technologies were used to analyze soil bacterial functional diversity and community structure, respectively. The results showed that the abundance, functional diversity (Shannon index, Simpson index and McIntosh index), and gene diversity (Chao1 index and ACE index) of bacterial community in control soil were higher than those in the three risk levels. The bacterial abundance, functional diversity index (Shannon index and McIntosh index) and gene diversity index (Chao1 index and ACE index) significantly decreased with the increasing RI levels. At the same RI level, the abundance, average well color development, functional diversity index, OTUs (Operational taxonomic units) numbers and gene diversity index (Chao1 index and ACE index) of bacterial community in Pb contaminated soil were significantly higher than those in Cd contaminated soil (P<0.05). However, the bacterial Simpson indices in Pb contaminated soil showed no significant differences with ones in Cd contaminated soil (P>0.05) at the same level. The utilization rate of carbohydrate and carboxylic acid compounds by bacteria in Pb contaminated soil were significantly higher than those in Cd contaminated soil at the same RI level. The principal component analysis (PCA) showed that the carbon source utilization efficiencies significantly correlated with the RI levels, and the efficiencies were significantly different between Pb and Cd contaminated soils at the same level. Proteobacteria, Actinobacteria, Acidobacteria and Chloroflexi were dominant in all treatments. The bacterial community composition varied under different RI levels. At the same level, we found the relative abundance of Proteobacteria were higher in Pb contaminated soils than in Cd contaminated soils, while the relative abundance of Chloroflexi were higher in Cd contaminated soil. There were also significant differences between the relative abundance of Brachyrhizobium, Sphingomonas, Streptomyces and norank_f__Roseiflexaceae, respectively, in Pb and Cd contaminated soil. Our results indicated that the TF values proposed by Hakanson should be adjusted during the process of evaluating the potential ecological risks of Pb and Cd to soil microorganisms. This paper underlied a new exploration to mediate the TF values.