Objective To understand the basic health condition of urban and rural residents in Chongqing and its influencing factors and to analyze the health inequity. Methods Demographic characteristics, two-week prevalence, chronic illness prevalence, and poor perceived health prevalence were calculated. Logistic regression analysis was adopted to analyze the effects of gender, age, education degree, income, medical insurance, and urban and rural area effects on the health of residents. The health inequity was evaluated according to the concentration index (CI) of controlled variables and health inequity index (HII). Results The demographic characteristics and health condition of urban and rural residents were different. Factors that influenced the health were gender, age, education degree, income, medical insurance, urban area, and rural area. The HII scores of two-week prevalence, chronic illness prevalence, and poor perceived health prevalence of rural residents were above 0.1. The HII scores of two-week prevalence and chronic illness prevalence of urban residents were above 0.1 and the HII of poor perceived health prevalence was under 0.1. Conclusion Health inequity exists between urban residents and rural residents. The influencing factors of health inequity are education degree, income, and medical insurance. The comprehensive evaluation result of HII is ideal.