The effects of long-term urbanization changes in obesity are unclear. Data were obtained from the China Health and Nutrition Survey (CHNS) 1989–2018. A multidimensional urbanicity index was used to define the urbanization level for communities. Group-based trajectory modeling was used to identify distinct urbanization change trajectories. Gender-stratified multilevel models were used to investigate the association between urbanization trajectories and weight/BMI, through the PROC MIXED procedure, as well as the risk of being overweight + obesity (OO)/obesity (OB), through the PROC GLIMMIX procedure. A total of three patterns of the trajectory of change in urbanization were identified in 304 communities (with 1862 measurements). A total of 25.8% of communities had a low initial urbanization level and continuous increase (termed “LU”), 22.2% of communities had a low–middle initial urbanization level and constant increase (termed “LMU”), and 52.0% of communities had a middle–high initial urbanization and significant increase before 2009, followed by a stable platform since then (termed “MHU”). During the 30 follow-up years, a total of 69490 visits, contributed by 16768 adult participants, were included in the analysis. In the period, weight and BMI were observed in an increasing trend in all urbanization trajectory groups, among both men and women. Compared with LU, men living in MHU were related to higher weight, BMI, and an increased risk of OO (OR: 1.46, 95%CI: 1.26 to 1.69). No significant associations were found between urbanization trajectories and OB risk in men. Among women, the associations between urbanization and all obesity indicators became insignificant after controlling the covariates. Obesity indicators increased along with urbanization in the past thirty years in China. However, the differences among urbanization trajectories narrowed over time. More urbanized features were only significantly associated with a higher risk of obesity indicators in Chinese men. The effects of urbanization on obesity among women were buffered.