Objective To compare the circulating fibroblast growth factor-23 (FGF23) levels between patients undergoing in-center nocturnal hemodialysis (INHD) and conventional hemodialysis (CHD), and to explore the factors influencing the level of circulating FGF23. Methods Limosis vein blood were collected from 44 patients undergoing INHD and 64 patients undergoing CHD in Changzheng Hospital, Second Military Medical University. Serum calcium, phosphate, intact parathyroid hormone (iPTH), urea clear index (Kt/V), 25-hydroxy vitamin D, ferritin, hemoglobin, blood lipid, and FGF23 were measured and compared between the two groups. All the influencing factors of FGF23 were analyzed by multivariate regression analysis. The correlations between FGF23 and serum calcium, phosphate, calcium-phosphate product, iPTH, 25-hydroxy vitamin D and Kt/V were analyzed by Pearson correlation analysis. Results The levels of serum phosphate and FGF23 in patients undergoing INHD were significantly lower than that in patients undergoing CHD (P<0.05). The dialysis adequacy of INHD was significantly higher than that of CHD (P<0.05). Serum FGF23 was related to serum calcium, serum phosphate, and calcium-phosphate product (all P<0.01), but not to iPTH or Kt/V. Conclusion INHD is more effective than CHD in improving the chronic kidney disease-mineral and parameters of bone abnormalities (CKD-MBD). Calcium-phosphate product is an independent influencing factor of serum FGF23 in patients undergoing IHND. Reducing the serum FGF23 by decreasing calcium-phosphate product may be a mechanism of INHD to improve the clinical prognosis of patients.