Connected asexual individuals (ramets) of clonal plants can transport and share resources such as water, nutrients, and photosynthates. Such clonal integration can enhance the capacity of ramets to tolerate environmental stresses, and thus may further affect the composition and biomass of soil microbial communities around the ramets. Although a large number of studies have examined the effects of clonal integration on the capacities of clonal plants to withstand stresses, very few have tested its influence on soil microbial communities. In a Phragmites australis wetland in the Yellow River Delta in China, we added 0, 5, and 10 mm crude oil per year to circular plots of 60 cm in diameter. In half of the plots, we severed the rhizome connections between the ramets of P. australis inside and outside the plots to prevent clonal integration, whereas the rhizome connections were kept intact in the other half to allow integration. The experiment lasted for two years from 2014 to 2015. We sampled soil in each plot in August, and measured the phospholipid fatty acids (PLFAs) of soil microbes and the carbon and nitrogen concentrations of the soil microbial biomass. Sampling time had a significant effect on total soil microbial PLFAs, carbon, and nitrogen, and these three variables were all higher in 2015 than in 2014. Crude oil addition significantly increased total PLFAs of soil microbes in 2015, but had little effect in 2014. Furthermore, crude oil addition resulted in a decrease in soil microbial carbon and nitrogen in 2014, but an increase in 2015. Clonal integration had no significant effect on soil microbial PLFAs, carbon, or nitrogen in either 2014 or 2015. Total soil microbial PLFAs were significantly positively related to soil microbial carbon and nitrogen. Therefore, crude oil contamination in wetlands can significantly affect the dynamics of soil microbes, whereas physiological integration of clonal plants may not.