Electrode materials that act through the electrochemical conversion mechanism, such as metal selenides, have been considered as promising anode candidates for lithium-ion batteries (LIBs), although their fast capacity attenuation and inadequate electrical conductivity are impeding their practical application. In this work, these issues are addressed through the efficient fabrication of MnSe nanoparticles inside porous carbon hierarchical architectures for evaluation as anode materials for LIBs. Density functional theory simulations indicate that there is a completely irreversible phase transformation during the initial cycle, and the high structural reversibility of β-MnSe provides a low energy barrier for the diffusion of lithium ions. Electron localization function calculations demonstrate that the phase transformation leads to high charge transfer kinetics and a favorable lithium ion diffusion coefficient. Benefitting from the phase transformation and unique structural engineering, the MnSe/C chestnut-like structures with boosted conductivity deliver enhanced lithium storage performance (885 mA h g-1 at a current density of 0.2 A g-1 after 200 cycles), superior cycling stability (a capacity of 880 mA h g-1 at 1 A g-1 after 1000 cycles), and outstanding rate performance (416 mA h g-1 at 2 A g-1).