Background: The association between selenium and chronic kidney disease (CKD) remains controversial. Population studies with large samples facilitate the reliability of conclusions. Objective: In this study, we aimed to describe the prevalence of a CKD association with selenium intake in middle-aged and older Chinese. Methods: Data for this study were obtained from the China Health and Nutrition Survey (CHNS). A total of 5381 participants (aged ≥ 45) with biochemical test data were included in the study. Logistic regression models were used to examine the association between diet selenium intake (quartile) and the prevalence of CKD. Results: A total of 942 (17.01%) participants had CKD. The prevalence of CKD was 23.33%, 20.32%, 14.98%, and 9.25% among participants with average selenium intakes of 21.5 ± 4.82, 33.1 ± 2.79, 43.8 ± 3.70, and 67.0 ± 13.97 µg/day, respectively. In the fully adjusted model (Model 3), across the quartiles of selenium intake, the ORs for the prevalence of CKD were 1.00, 1.09 (95% CI 0.69–1.73), 0.82 (95% CI 0.49–1.38), and 0.43 (95% CI 0.22–0.85). The protein intake had a certain diagnostic significance for the selenium intake. Conclusions: An adequate selenium intake may have a positive effect on CKD. The influence of individual weight and location on the effect of selenium on CKD needs to be further explored.