To understand the distribution and infection status of hantavirus in Myomorph rodents on Bolshoy Ussuriysky Island (Heixiazi Island) at the Sino-Russian border, and to provide data for the safe development and utilization of Bolshoy Ussuriysky Island. In 2013 and 2014, Myomorph rodents were trapped on Bolshoy Ussuriysky Island. Total RNA was extracted from rodent tissue, and it was screened for hantavirus RNA by using reverse transcription-polymerase chain reaction. Univariate and multivariate nonconditional logistic regression analysis was used to analyze the RNA prevalence rates in eight species of rodents, in relation to species, sex, age, habitat, and season. In addition, PCR amplicons were sequenced and phylogenetic analysis was performed by using Mega 5.1 software. Six hundred forty-four rodents belonging to three orders, five families, and eight genera were trapped. Fifty-two rodents were infected with hantavirus, and the rate of RNA detection was 8.07%. The infection rates of rodents in different habitats (χ2 = 14.853, p < 0.05) and different seasons (χ2 = 16.990, p < 0.05) showed significant differences. A logistic regression analysis showed that habitat and trapping season were risk factors of hantavirus infection (p < 0.05). Phylogenetic analysis showed that the gene sequences of positive samples were Hantaan virus and Khabarovsk virus. There are two types of hantaviruses, such as HTNV (in Apodemus agrarius, Clethrionomys rutilus, Microtus fortis, Rattus norvegicus) and KHAV (in C. rutilus), among the rodents on Bolshoy Ussuriysky Island, and season and habitat are risk factors of hantavirus infection.