Abstract Li 3 YCl 6 is a promising candidate for solid electrolytes (SEs) in all-solid-state Li-ion batteries due to its high ionic conductivity, electrochemical stability, and compatibility with metal-oxide electrodes. The monoclinic and trigonal crystal structures of Li 3 YCl 6 with space groups C2/c and P-3m1 have been studied extensively, while little attention has been given to the trigonal P-3c1 phase (space group no. 165). Additionally, Li-ion diffusion mechanism in 3d transition metal (TM) substituted compounds along with their structural stability are interesting to study. Therefore, we investigate the Li diffusion mechanism in Li 3 YCl 6 and TM substituted Li 3 YCl6 in the P-3c1 phase using first-principles calculations. We have found that all the substituted compounds are thermodynamically stable at room temperature and show high oxidation stability. Li 3 Y 0.875 Co 0.125 Cl 6 exhibits the lowest activation energy (0.11 eV) for Li-ion diffusion and the highest Li-ion mobility ( σ = 0.39 mS cm −1 at room temperature), which is strongly anisotropic. We used the Crystal Orbital Hamilton Population method to analyze the bonding characteristics of Li 3 YCl 6 and 3d TM substituted Li 3 YCl 6 and found that the Co–Cl bond is weaker than the Cr–Cl bond. This may explain the lower activation energy observed for Li 3 Y 0.875 Co 0.125 Cl 6 . Our results provide insights into the substitution effect in Li 3 YCl 6 superionic conductors, which could guide the design and development of high-performance SEs for Li-ion batteries.