Multidisciplinary team-based integrated care (MDC) has been recommended for patients with chronic kidney disease (CKD). However, team-based specific structured care systems are not yet established. Therefore, we investigated the efficacy of MDC system and the optimal number of professionals that make up the team for maintaining kidney function and improving prognosis. Methods: This nationwide, multicenter, observational study included 2,957 Japanese patients with CKD who received MDC from 2015 to 2019. The patients were divided into four groups according to the number of professionals in the MDC team. Groups A, B, C, and D included nephrologists and one, two, three, and four or more other professionals, respectively. Changes in the annual decline in estimated glomerular filtration rate before and after MDC were evaluated. Cox regression was utilized to estimate the correlation between each group and all-cause mortality and the start of renal replacement therapy (RRT) for 7 years. Results: The change in eGFR significantly improved between before and at 6, 12, and 24 months after MDC in all groups (all p < 0.0001). Comparing group D to group A (reference), the hazard ratio (HR) for all-cause mortality and the start of the RRT was 0.60 (95% confidence interval, 0.48–0.73; p < 0.0001) after adjustment for multiple confounders. Lower HR in group D was confirmed in both diabetes and nondiabetes subgroups. Conclusion: An MDC team comprised of five or more professionals might be associated with improvements in mortality and kidney prognosis. Furthermore, MDC might be effective for treating CKD other than diabetes.