Objective To investigate the impact of reducing stray dog population on the prevalence of Echinococcus spp. in small mammals. Methods From April 2016 to June 2020, stray dogs were captured and euthanized by professional dog catchers or by the public service department, in Shiqu County of Ganzi Tibetan Autonomous Prefecture throughout the year. During 2015 to 2020, investigators drove along the highway from State-owned livestock farm to Niga Township (130.5 km) in Shiqu County, and recorded the number of stray dogs within the sight distance on both sides of the highway. The density of stray dogs in Shiqu County was calculated by dividing the number of stray dogs by the driving distance. Small mammals were captured in Edoma, Wenbo, Yiniu, Xiazha, Niga, Mengyi and Gemeng Townships of Shiqu County and dissected on-site in July 2016 and July-August 2020. Organs of small mammals were stored in 95% ethanol and transferred back to laboratory. Hydatid lesion-like tissues were sampled from the organs for extraction of genomic DNA for PCR to amplify cytochrome c oxidase subunit 1 (cox1). The amplified products of PCR were sequenced and then compared with the known sequences in GenBank through BLAST to determine the species of Echinococcus. The infection rate of Echinococcus in small mammals was calculated according to the sequencing and alignment results. The 95% confidence interval of the rate was calculated using the Clopper & Pearson exact method. The difference in the prevalence of Echinococcus in small mammals was analyzed by chi-square test or Fisher exact test. Results From April 2016 to June 2020, 41 446 stray dogs were captured and euthanized in Shiqu County, including 26 570, 4 377, 5 656, 4 100, and 743 in each year, respectively. The density of stray dogs in Shiqu from 2015 to 2020 was 0.80, 0.04, 0.06, 0.04, 0.05 and 0.05 per kilometer, respectively. In July 2016, a total of 261 small mammals were captured, including 192 pikas (Lagomorpha : Ochotonidae) and 69 voles (Rodentia : Cricetidae). There were 14 small mammals infected with Echinococcus, of which 8 were voles and 6 pikas. The infection rate of E. multilocularis metacestodes in voles in 2016 was 11.6% (8/69, 95% CI: 5.1%-21.6%). The infection rate of E. multilocularis metacestodes and E. shiquicus metacestodes in pikas in 2016 were both 1.6% (3/192, 95% CI: 0.3%-4.5%). From July to August of 2020, a total of 270 small mammals were captured, of which 223 were voles and 47 pikas. The infection rate of E. multilocularis metacestodes in voles in 2020 was 0.5% (1/223, 95%CI: 0-2.5%). No pikas were found to be infected with Echinococcus spp.. The prevalence of E. multilocularis metacestodes in voles in 2020 was significantly reduced compared with that in 2016 (P < 0.01). The infection rate of E. multilocularis metacestodes and E. shiquicus metacestodes in pikas in 2020 were both lower than that in 2016, but the difference was not statistically significant (P > 0.05). Conclusion In endemic areas where stray dogs play an important role in the transmission of E. multilocularis, measures to reduce the density of stray dogs can significantly lower the infection rate of E. multilocularis metacestodes in voles.