This study aims to develop high-capacity hard carbon anode materials for alkali-ion batteries by controlling the microstructures of non-graphitic hard carbon through an annealing protocol and investigating the effects on the alkali-ion storage mechanisms using physical, chemical, and electrochemical analytical techniques. The hard carbon materials were synthesized at temperatures ranging from 900 °C to 1600 °C. Those synthesized at 1100 °C with high surface area and abundant defects exhibited the highest reversible capacity in Li- and K-ion systems, with the storage dominated by surface-adsorption mechanisms. In contrast, the hard carbon compounds prepared at 1400 °C with numerous curve-featured pores delivered the highest reversible capacity in the Na-ion system, indicating that these pores are the preferred Na-ion storage sites, particularly in low-voltage plateau regions. This study provides a comprehensive understanding of the relationship between microstructures and alkali-ion storage mechanisms in non-graphitic hard carbon and highlights the importance of tailoring the microstructures of hard carbon to achieve high specific capacity for the desired alkali-ion species.