Heterogeneous Fenton-like catalysis is a widely used method for the degradation of organic pollutants. However, it still has some limitations such as low activity in the neutral condition, low conversion rates of metals with different valence states, and potential secondary metal pollution. In this study, a Fenton-like nanocatalyst was first created by generating ultrasmall copper nanoclusters (Cu NCs) on the surface of hydroxyapatite (HAp) through a process of doping followed by modification. This resulted in the formation of a composite nanocatalyst known as Cu NCs/HAp. With the help of hydrogen peroxide (H 2 O 2 ), Cu NCs/HAp exhibits an outstanding Fenton-like catalytic performance by efficiently degrading organic dyes such as methylene blue under mild neutral conditions. The removal rate can reach over 83% within just 30 min, demonstrating ideal catalytic universality and stability. The improved Fentonlike catalytic performance of Cu NCs/HAp can be ascribed to the synergistic effect of the multivalent Cu species through two simultaneous reaction pathways. During route I, the embedded Cu NCs with a core−shell Cu 0 /Cu + structure can undergo sequential oxidation to form Cu 2+ , which continuously activates H 2 O 2 to generate hydroxyl radicals ( • OH) and singlet oxygen ( 1 O 2 ). In route II, Cu 2+ produced from route I and initially adsorbed on the surface of HAp can be reduced by H 2 O 2 , thus regenerating Cu + species for route I and achieving a closed-loop reaction. This work has confirmed that Cu NCs loaded on HAp may be an alternative Fenton-like catalyst for degradation of organic pollutants and environmental remediation, opening up new avenues for potential applications of other Cu NCs in future water pollution control.