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Background Genital tract infections with ureaplasma urealyticum (UU) and chlamydia trachomatis (CT) are the most frequent sexually transmitted infections (STIs). The aim of this study is to understand the prevalence of UU and CT among general internal married migrants and to explore some possible influencing factors, so as to provide some evidences for STIs prevention in China. Methods A cross-sectional study was conducted in three cities of China from March 2016 to February 2017. A total of 3180 internal-married migrants were included. The structured questionnaire survey, gynecological or andrology examination and laboratory detection were conducted by the trained research fellow s. The prevalence of UU and CT was laboratory-confirmed in this study. Results The prevalence of laboratory-confirmed UU and CT were 45.41%, 5.75%, respectively. The co-infection rate was 4.09%. The rates of UU and CT of Shanghai participants (54.01%, 7.35%) were the highest, and the lowest were that of Yinchuan (37.74%, 4.52%). In Urumqi, the prevalence of UU and CT were 44.77%, 5.42%, respectively, but it has the highest co-infection rate. The multiple stepwise logistic regressions found that the prevalence of UU among three cities were different, and the male’s UU infection was lower than that of women (OR=0.71, 95%CI:0.61-0.83), and the 20-34 age group participants had lower UU and CT risk, compared with that of 45-49 age group. Moreover, the white-collar workers had lower risk of UU infection (OR=0.64, 95%CI: 0.49-0.83), compared with laborer, and using condom could reduce the UU infection (OR=0.74, 95%CI: 0.63-0.87). Compared with urban migrants, the rural participants had higher risk of CT infection (OR=1.68, 95%CI: 1.12-2.52), and sex behavior during menstruation could increase the prevalence of CT (OR=1.49, 95%CI: 1.05-2.11). Conclusion The prevalence of UU and CT were high and the co-infection was also serious among general internal married migrants. More health promotion measures about UU and CT should be taken to help general migrants of China, especially women and those with lower social-economic status (laborers from rural area), risky sexual behaviors such as having sex during menstruation should be warned of and condom-use should be promoted.