The selective adsorption of small molecules over specific facets plays an important role in morphology controlled synthesis of metal nanocrystals. In the present work, hydrogen is found to be a good capping agent for direct synthesis of branched nickel nanocrystals, i.e., secondary branching (Ni-SB) nanoparticles and multipods (Ni-MP). Using ab initio thermodynamics and the Wulff construction principle, it has been found that: (i) in the presence of hydrogen (P_H2 = 6 bar), the facet structure stability follows the order of Ni(100) > Ni(111) > Ni(110), resulting in competitive over-growth along the 〈111〉 and 〈110〉 directions; (ii) with increasing hydrogen pressure, the Ni deposition rate over the crystal surface increases as a result of more Ni²⁺ reduction; the competition between deposition and surface diffusion, therefore, becomes the vital factor for the nanocrystal growth process; (iii) the diffusion energy barrier of a surface Ni atom on Ni(111) is lower than that on Ni(110), especially on hydrogen covered surfaces, indicating that the kinetic over-growth only along the 〈111〉 direction producing Ni-MP will be dominant under P_H2 = 14 bar; (iv) the ab initio based Wulff construction principle predicts the shapes and morphologies at different hydrogen pressures which is further confirmed with HRTEM results. Finally, compared with nickel nanoparticles (Ni-NP) synthesized in the absence of hydrogen, the hydrogen assisted branched Ni nanomaterials, especially the Ni-MP, show higher catalytic activities for hydrogenation reactions of acetophenone and nitrobenzene.