Objective To understand the prevalence of chronic diseases among the rural elderly in Yulong County and Fumin County of Yunnan Province, explore and analyze the relationship between elderly chronic diseases and physical labor intensity, and provide targeted prevention and control strategies for the prevention and treatment of elderly chronic diseases. Methods Multi-stage stratified random sampling method was used in this survey and the elderly 2 299 elderly people aged ≥60 years in rural areas of Yulong County and Fumin County of Yunnan Province were selected. The elderly aged 60 years and above were investigated with questionnaires and physical examinations on the prevalence of 10 chronic diseases, including diabetes, hypertension, coronary heart disease, stroke, COPD, asthma, hyperlipidemia, chronic kidney disease, gastrointestinal ulcer, and cataract. Descriptive analysis, χ2 test and multivariate logistic regression analysis were used to analyze the influencing factors. Results There were statistically significant differences between different ethnic groups in whether they have read books, whether they live alone, whether they are farmers, whether they are physical labor intensity, and whether they are obese (χ2 test, P < 0.05). The prevalence of chronic diseases in the elderly was 83.3%, of which the prevalence of chronic diseases in the Han nationality was 83.1%, and the prevalence of chronic diseases in the Naxi nationality was 83.6%. With the increase of age, in addition to the decline in the prevalence of chronic diseases in the population aged 75 and over, the prevalence of chronic diseases in the elderly population in the surveyed areas showed an upward trend, and the difference was statistically significant (χ2 test, P < 0.05). Central obesity was a risk factor for chronic diseases in the elderly. The risk of chronic diseases in elderly people with central obesity was 1.895 times that without central obesity. The moderate-intensity physical labor was a protective factor for elderly chronic diseases. The risk of chronic disease of moderate-intensity physical labor was 0.643 times that of low-intensity physical labor, and the difference was statistically significant (P < 0.05). With the increase of age, the proportion of high-intensity physical labor showed a downward trend, and the proportion of light-intensity physical labor showed an upward trend, and the difference was statistically significant (χ2 test, P < 0.05). Conclusions Central obesity and physical labor intensity are the influencing factors of chronic diseases in the elderly. There are differences in physical labor intensity with the increase of age, suggesting that to prevent chronic diseases in the elderly, it is necessary to continue to do a good job in health education for the elderly in terms of lifestyle and to further prevent the aging occurrence of chronic diseases. [ABSTRACT FROM AUTHOR]