Objective: To explore the transmission of integrase inhibitors (InIs) resistant strains among newly diagnosed HIV-1 infected individuals in Shenyang city. Methods: Eighty newly diagnosed HIV infected individuals were retrospectively collected in Shenyang from June 2018 to March 2019. The sequences of integrase-encoding genes were amplified from the viral RNA in plasma. The viral genotypes were analyzed with phylogenetic method and the mutations of drug resistance genes were interpreted according to the algorithm of Stanford HIV drug resistance database. The primary drug resistance rates were calculated and natural polymorphisms on InIs resistance sites in different subtypes of the virus strain were analyzed. Results: Among the 80 HIV-1 infected individuals, 51, 14 and 6 cases were genotyped as HIV CRF01_AE, CRF07_BC and subtype B respectively, accounting for 63.8%,17.5% and 7.5%. Nine cases (11.3%) were classified as atypical HIV-1 recombinants. R263K mutation was detected in two CRF01_AE infected patients, and E138A mutation was detected in a patient infected with subtype B. The overall drug resistance rate for InIs was 3.8%. CRF01_AE infected individuals showed amino acid polymorphism at the site 50, 74, 119 and 153 relevant to InIs resistance with frequency of 5.9%, 2.0%, 13.7% and 4.0% respectively. The CRF07_BC infected individuals showed amino acid polymorphism at the site 50, 74 and 157 relevant to InIs resistance with frequency of 7.1% for each site. Conclusion The primary drug resistance rate of InIs among the newly diagnosed HIV infected people in Shenyang was low, but a small number of patients showed amino acid polymorphisms on InIs resistance sites. To interpret the significance of drug resistance mutations in InIs better, it is necessary to strengthen both the monitoring of HIV InIs resistance and the study on the drug resistance-relevant genotype and phenotype of HIV-1 strains epidemic in China.