Sodium–selenium (Na–Se) and potassium–selenium (K–Se) batteries have emerged as promising energy storage systems with high energy density and low cost. However, major issues such as huge Se volume changes, polyselenide shuttling, and low Se loading need to be overcome. Although many strategies have been developed to resolve these issues, the relationship between the carbon host pore structure and electrochemical performance of Se has not been studied extensively. Here, the effect of the carbon host pore structure on the electrochemical performance of Na–Se and K–Se batteries is investigated. N, S-co-doped hierarchically porous carbon microspheres with different pore structures that can incorporate a large amount of amorphous Se (∼60 wt %) are synthesized by spray pyrolysis and subsequent chemical activation at different temperatures. By optimizing the amount of micropore volume and micropore-to-mesopore ratio, high reversible capacity and cycling stability are achieved for the Se cathode. The optimized cathode delivers a reversible capacity of 445 mA h g–1 after 400 cycles at 0.5C for Na–Se batteries and 436 mA h g–1 after 120 cycles at 0.2C for K–Se batteries. This study marks the importance of developing conductive carbon matrices with delicately designed pore structures for advanced alkali metal–chalcogen battery systems.