Potential effects of antibiotics on agricultural soil microflora have recently become increasing concerns with antibiotic-contaminated biosolid now being used in agricultural land. However, changes of soil microbial community function caused by the antibiotic-associated disturbance are less addressed. This paper investigated the changes in microbial functional diversity by spiking sulfamethoxazole (SMX) and chlortetracycline (CTC) in a loam paddy soil and then incubating for 21 days. The dose-effect and time-dependent changes of antibiotic-associated disturbance on soil microbial community were analyzed with the soils sampled at 7 and 21 days using Biolog EcoPlate. At day 7 following treatment, SMX decreased functional diversity of soil microbial community, and the treatment of 100 mg SMX kg(-1) dry soil had a significant inhibition of average well color development (AWCD) and Shannon index as compared to the control (p < 0.05). The SMX changed to improve soil microbial community function at day 21. CTC had less effect on soil microbial community function during the whole incubation period. Antibiotic dissipation and adsorption in soil, which may decrease their microbial bioavailability, led to the temporary change of antibiotic effect on functional diversity of soil microbial community. Principal component analysis clearly revealed the difference of antibiotic dose-effects on the soil microbial community function. The findings demonstrated that soil microbial community showed more sensitivity to SMX than CTC, and soil microbial community function could recover or improve due to antibiotic dissipation in soil.