Objective To preliminary study of the resistance mechanisms of S.pneumoniae(S.pn) by determining the resistance rates and gene of S.pn isolated from the lower respiratory tract infection infants. Methods Drug susceptibility test with disk diffusion and broth micro-dilution was conducted to evaluate the resistance rates of 73 strains of S.pn isolated from the lower respiratory tract infection infants to penicillin, levofloxacin and other 10 antibiotics. PCR method was used to analysis the antimicrobial resistant genes tet M, mef A, erm A, erm B and int Tn of the isolates. Results The antibiotic resistance rates of the S.pn isolates to erythromycin, clindamycin and tetracycline were 95.9%, 94.5%, 87.7% and 0% to vancomycin when tested with disk diffusion method. The antibiotic resistance rates of these isolates to penicillin, cefotaxime and ceftriaxone were 45.2%, 47.9% and 46.6% respectively when tested with broth micro-dilution method. The carrier frequencies of tet M, mef A, erm A, erm B, int Tn genes in the 73 isolates were 91.8%, 63.0%, 58.9%, 39.7% and 61.6% respectively. Conclusion The S.pn strains isolated from infant respiratory tract in Chengdu perform a serious drug resistance problem, especially to routine antibiotics like erythromycin, clindamycin and tetracycline and cephalosporin, the resistance rate to levofloxacin, chloramphenicol remained at a low level; the resistance to tetracycline was closely related with the tet M gene fragment, the resistance to macrolide was mainly decided by active efflux pump and secondarily by the alternation of gene targeting, int Tn had close relation with tet M, erm B.