To investigate the development trajectory of chronic diseases among menopausal women and its influencing factors, and to provide a reference basis for the health management of menopausal women, this study utilized five waves of data (2011-2020) from the China Health and Retirement Longitudinal Study (CHARLS). A total of 3,508 women aged 40–54 at baseline were selected as subjects. Group-based trajectory modeling (GBTM) was employed to identify their chronic disease developmental trajectories, with further subgroup analysis conducted by birth cohort. Multinomial logistic regression was used to analyze the factors influencing the trajectory classifications. The results showed that the developmental trajectories of chronic diseases in menopausal women can be categorized into three types: low-level slow growth (22.59%), medium-level steady growth (60.05%), and high-level rapid growth (17.36%). Trajectory analysis grouped by birth cohort also revealed the same three categories. Compared to the 1957–1961 birth cohort, the 1962–1971 birth cohort had a higher proportion belonging to the low-level group and a lower proportion belonging to the high-level group. Logistic regression indicated that menopausal status, sleep, smoking, and employment status were the main influencing factors for trajectory classification (P < 0.05). The developmental trajectories of chronic diseases in menopausal women are heterogeneous. Stratified interventions should be implemented, alongside strengthening health education on chronic disease prevention and management, and providing personalized health services to facilitate a smooth menopausal transition.