Methane dry reforming (MDR) to syngas over Ni-based catalyst is a sustainable process with a small ecological footprint by efficient utilization of two abundant greenhouse gases. The deactivation of Ni-based catalysts due to coke deposition and nickel sintering is a serious obstacle to the industrialization process. Herein, homemade hydroxyapatite (HAP) nanorods with enriched [Ca–O–P] sites were synthesized. Moreover, Ni-substituted HAP catalysts with extremely low Ni loading were prepared by facile wet impregnation, which simultaneously could obtain rich [Ni–O–P] sites and CaO basic sites by Ni2+ substituting for Ca2+ in the structure of [Ca–O–P]. The synergy of [Ni–O–P] sites and CaO basic sites associated with [Ca–O–P] sites on hydroxyapatite nanorods enables a high specific activity of 40.5 molCH4·gNi–1·h–1 with a negligible amount of coke deposition as a catalyst for MDR at 600 °C, a temperature that is thermodynamically more prone to coke formation. Density functional theory calculations confirmed that the existence of Ni cations in the form of [Ni–O–P] is beneficial for CH4 activation. In contrast, when commercial hydroxyapatite is used as the support, the obtained catalyst shows poor activity and stability. The special interaction between Ni and HAP can provide inspiration for future catalyst design in heterogeneous hydrocarbon catalysis processes.