Alkaline water electrocatalysis is considered as one of the most reliable method to prepare the stable, inexpensive, and sustainable water splitting catalyst in large-scale. Recently, MoSe2 attracted great attention as a promising catalyst because of its high electrochemical activity and earth-abundant nature. In this paper, bionic NixSey/MoSe2 coralline-liked heterogeneous structures were successfully prepared on 3D nickel foam (NF) via a simple solvothermal process complemented by hydrothermal strategy with selenization and alkali treatment. Furthermore, to overcome the less active sites and poor electrical conductivity of MoSe2, we learned from the coral structure for the inspiration, and reported a novel hollow rod-like structure with increased active sites. Also, 1 T-2H MoSe2 improved the electrical conductivity of single phase MoSe2. We first confirmed the multi-phase of catalyst by XPS analysis with Mo 3d5/2 splited into two independent regions with the 2H and 1 T phase transition. The optimal ratio of NixSey/MoSe2/NF-5 exhibited excellent electrocatalytic activity towards HER in 1 M KOH, driving current densities of 10, 100 and 200 mA cm−2 at only 76, 165 and 194 mV with stability over 24 h. The work provides new ideas for the construction of transition metal selenides hollow rod array structures of efficient HER electrocatalysts.