Regular physical activity is beneficial for both physical and mental health. However, studies on physical activity levels among middle-aged and elderly individuals in China are relatively scarce, and the association between different activity levels and certain chronic diseases remains unclear. Using cross-sectional data from the 2020 China Health and Retirement Longitudinal Study (CHARLS), this study describes the prevalence of chronic diseases and examines their associations with physical activity (PA). Participants self-reported the presence of fifteen chronic health conditions: hypertension, dyslipidemia, diabetes, cancer, chronic lung diseases, liver disease, heart attack, stroke, kidney disease, stomach diseases, emotional and mental issues, memory-related diseases, Parkinson’s disease, arthritis or rheumatism, and asthma. Total physical activity was assessed through self-reports using instruments similar to the International Physical Activity Questionnaire (IPAQ). Multivariate logistic regression was used to estimate the association between chronic diseases and PA. In China, more than one-sixth of middle-aged and elderly individuals do not meet physical activity guidelines. Compared to those with low PA, individuals with moderate PA were associated with a lower prevalence of four chronic diseases (heart disease, stroke, emotional and mental issues, asthma), while those with high PA were associated with a lower prevalence of nine chronic diseases (hypertension, dyslipidemia, diabetes, cancer, heart attack, stroke, emotional and mental issues, memory-related diseases, asthma). Higher physical activity levels are associated with lower odds of chronic diseases. These associations between physical activity and various chronic diseases are inconsistent. Future research should employ cohort or experimental studies to determine the causal relationships between physical activity and the prevalence of different chronic diseases.