Doping hetero-atoms into non-noble metal phosphides is an important strategy for enhancement of hydrogen evolution reaction (HER) performance. Herein, we prepare a self-supported F-doped CoP/Ni2P nanowire arrays grown on Ni foam by using a strategy with three steps including hydrothermal reaction, fluorination, and low-temperature phosphorization. The F-CoP/Ni2P nanowire consists of a well-defined crystalline core and a thin amorphous surface layer. The F-doping and amorphous surface layers effectively expose a large number of active sites, optimize the electronic configuration of Ni, Co and P on the surface, and promote the electron transport performance. As a result, the prepared F-CoP/Ni2P@NF-II exhibits excellent electrocatalytic activity for HER in alkaline electrolyte with a lower overpotential of 75 mV at 10 mA cm−2, a small Tafel slope of 54.8 mV dec−1, and good durability. This work provides a simple method for developing transition metal phosphate-based catalysts towards hydrogen evolution reaction.