Objective To understand the drug-resistance of patients with HIV antiviral therapy in Fuyang and provide the basis for effective antiviral therapy. Methods A total of 253 cases of HIV/AIDS patients with antiviral treatment over 12 months and viral load ≥ 1000cps/ml in 2016 were collected. Nested PCR was used to amplify, sequenced and identify the subtypes, and to compare it to the international drug bank to determine the level of resistance and the mutation of drug resistance genes. Results A total of 216 cases of effective gene sequence were identified with the B subtype (83.3%) and CRF01 AE subtype (10.2%), and there were significant differences in the subtype distribution between different infective modes. Drug-resistance in 87 patients, and the drug-resistance rate of HIV-1 virus was 40.28%. The occurrence of drug-resistance was significantly associated with the route of transmission, the baseline CD4, and use and replace of the second line treatment scheme. 21.1% patients were directed against NRTI mutation, and the highest mutation rate was M184V. 41.66% patients were directed against NNRTI mutation. The highest mutation rate was K103N, and the Gene mutation in PR region was produced in 2 cases (0.9%), with the main gene mutations of M46I, I54V and V82A in 1 case. 50.6% of drug-resistant patients were resistant to class NNRTI and NRTI, while 10.3% of the patients were all resistant to 11 reverse transcriptase inhibitors. Conclusion The general drug-resistance of HIV-1 virus in Fuyang was low, but cross resistance was serious in patients who had been resistant to drug.A few patients were resistant to all reverse transcriptase with a drug-resistant strain for PI. Drug-resistance monitoring should be strengthened, so as to adjust the treatment plan in time and improve the effect of treatment.