Objective To study the drug resistance characteristics of Diarrheagenic Escherichia coli (DEC) isolated from patients with diarrhea in two sentinel hospitals in Shunyi district of Beijing during 2013—2019. Method Stool samples of diarrhea patients were collected in the two sentinel hospitals during this period. Isolation, bacterial identification and PCR typing were conducted for DEC strains. Antimicrobial susceptibility tests were carried out using micro broth method to analyze the drug resistance characteristics of the isolated strains, including resistance rate, non-sensitive rate, multi-drug resistance rate and drug resistance spectrum. Result The detection rate of DEC in diarrhea patients was 9.53% (232/2434). The proportions of Enterotoxic Escherichia coli (ETEC), Enteropathogenic Escherichia coli (EPEC), and Enteroaggregative Escherichia coli (EAEC) were 56.47% (131/232), 27.16% (63/232) and 16.38% (38/232), respectively. The multi-drug resistance rates of DEC with 90 drug resistance spectrum, ETEC with 36 drug resistance spectrum, EPEC with 42 drug resistance spectrum, and EAEC with 23 drug resistance spectrum were 33.19% (77/232), 17.56% (23/131), 58.73% (37/63), 44.74% (17/38), respectively. Antibacterial drugs with resistance rate ≥30% included nudicacid (NAL) and ampicillin (AMP) for ETEC; AMP, tetracycline (TET), sulfamethoxazole tablets (SXT), sulfamethoxazole (Sul), NAL for EPEC; NAL, AMP, SXT, Sul, TET for EAEC. A comparison of the differences in the antimicrobial susceptibility tests during 2013—2016 and during 2017—2019 found that the resistance of ETEC to AMP, cefazolin (CFZ), TET, cefepime (FEP), aztreonam (AZM), and ampicillin/sulbactam (AMS) increased, while the resistance to Sul decreased; the resistance of EPEC to gentamicin (GEN) decreased; the resistance of EAEC to cefotaxime (CTX), GEN, and doxycycline (DOX) decreased. Conclusion Among the diarrhea cases in Shunyi, the intensity of DEC spread was high, and the spread and the drug resistances of ETEC, EPEC and EAEC had unique characteristics. The drug resistance was serious, to which close attention should be paid.