Abstract Background and Aims Extended-hours hemodialysis (HD) has better clinical outcomes than conventional HD. Previous studies have shown that a prolonged dialysis treatment time is associated with lower serum phosphorus levels, but the impact of extended-hours HD on calciprotein particles (CPP) is unknown. We investigated whether extended-hour HD and conventional HD have varying effects on blood levels of CPP and phosphorus, which have been identified as the main pathogenic molecules for vascular calcification. Method We performed a cross-sectional study of patients with extended-hours HD or conventional HD between January and March 2020. Blood CPP levels were measured in plasma and serum predialysis samples using a previously reported "gel filtration method". Linear and nonlinear associations between CPP and serum phosphorus levels were examined across dialysis modalities. Results A total of 382 participants (185 with extended-hours HD and 197 with conventional HD) were included in the analysis. The median age of participants was 71 years, 65% of the patients were men, and the mean phosphorus level was 5.4 mg/dL. Extended-hours HD was associated with lower plasma CPP levels (Extended-hours HD vs Conventional HD; 40,018 AU vs 75,728 AU) and serum CPP levels (Extended-hours HD vs Conventional HD; 66,524 AU vs 100,812 AU), regardless of similar serum phosphorus levels. Multivariable linear regression analysis showed that extended-hours HD was associated with lower natural logarithmic plasma CPP levels: -0.64 (95% CI: -0.74 to -0.55). Restricted cubic spline function indicated that extended-hours HD was associated with lower plasma CPP levels across levels of serum phosphorus, with significant differences observed between groups, especially in hyperphosphatemic conditions (P for interaction <0.01). Conclusion The patients with extended-hours HD had lower CPP levels than those with the conventional HD group despite no significant differences in serum phosphorus levels, which may contribute to better clinical outcomes in patients on extended-hours HD.