BackgroundThe Woman’s Condom, a newly designed condom for women, has obtained market approval in China, but it remains relatively unfamiliar to the migrant population. The aim of this study is to evaluate the short-term acceptability of the Woman’s Condom and influencing factors among internal migrants.MethodsA longitudinal study was conducted among 1800 migrants in Beijing, Chongqing, and Shanghai in China between August 2013 and August 2014.Three-level model was implemented with the Statistical Analysis System software (v.9.4 SAS Institute) to analyze within-individual changes, between-individuals effects, and between-group effects.ResultsThree-level model analysis revealed statistically higher short-term acceptability of the Woman’s Condom among subjects who lived in Shanghai (β = 6.50, t = 2.76, p < 0.01), unmarried and not in a cohabiting relationship (β = 3.05, t = 2.76, p < 0.01) than those who lived in Beijing, married and in a cohabiting relationship. Female (β = − 1.69, t = − 7.55, p < 0.01) and lower educational attainment (β = − 2.30, t = − 1.94, p = 0.05) were negatively related, while occupations of education, health, and civil staff (β = 1.50, t = 2.92, p < 0.01) were positively related to acceptability. It was predicted that migrants’ acceptability of the Woman’s Condom would significantly increase over time (β = 1.09, t = 5.54, p < 0.01).ConclusionsThe findings indicate that the Woman’s Condom enjoyed relatively high short-term acceptability among migrants in China. In order to popularize the Women’s Condoms in migrants, more publicity, consultation and training in open and prosperous areas should be strengthened.