We evaluated the interactive effects of nutrition education (NE) and lifestyle factors on kidney function parameters and cardiovascular risk factors among chronic kidney disease (CKD) patients. This cross-sectional cohort study recruited 2176 CKD stages 3–5 patients aged > 20 years from Integrated Chronic Kidney Disease Care Network, Shuang Ho Hospital, Taiwan between December 2008 and April 2019. The multivariable regression analysis was performed to investigate the interactive effects of NE with lifestyle factors on kidney function parameters and cardiovascular risk factors. Relative excess risk due to interaction (RERI) and attributable proportion (AP) were applied to assess additive interaction. Patients who were smoking or physically inactive but received NE had better estimated glomerular filtration rate (eGFR) (β: 3.83, 95% CI: 1.17–6.49 or β: 3.67, 95% CI: 2.04–5.29) compared to those without NE. Patients with smoking and NE significantly reduced risks for having high glycated hemoglobin A_1c (HbA_1c) by 47%, high low-density lipoprotein cholesterol (LDL-C) by 38%, and high corrected calcium (C-Ca) by 50% compared to those without NE. Moreover, NE and smoking or inactive physical activity exhibited an excess risk of high C-Ca (RERI: 0.47, 95% CI: 0.09–0.85 for smoking or RERI: 0.46, 95% CI: 0.01–0.90 and AP: 0.51, 95% CI: 0.03–0.99 for physical activity). Our study suggests that CKD patients who were enrolled in the NE program had better kidney function. Thus, NE could be associated with slowing kidney function decline and improving cardiovascular risk factors.