The present work focuses on the structural stability upon hydrogenation of three typical La–Mg–Ni-based alloys: La2MgNi9, La3MgNi14 and La4MgNi19. Structural changes during gaseous and electrochemical cycles were characterized, and the influence of the structure distortion on the hydrogen storage properties was concerned. Hydrogen-induced amorphization (HIA) and disproportionation of the three alloys have occurred during both the gaseous and electrochemical cycles. Structural stability of the phase structures in the La–Mg–Ni system is found to follow the order: LaNi5 > (La,Mg)5Ni19 > (La,Mg)2Ni7 > (La,Mg)Ni3 > (La,Mg)Ni2. HIA increases thermal stability of the metal hydrides and difficulty to dehydrogenation and leads to degradation of both the gaseous and electrochemical capacities. Interestingly, La2MgNi9 with poor stability presents elevated discharge capability even at 60 °C which can be attributed to increase in the hydrogen desorption capability and inhibition of the self-discharge induced by severe HIA at higher temperatures. In addition, HIA in the electrochemical reactions is obviously weaker than the extent during the gaseous cycles, which is mainly due to the slower hydrogenation speed. The development of HIA in the gaseous and electrochemical process is considered to follow the direct and gradual modes, respectively.