Molybdenum nitride-based materials have been extensively investigated as pseudocapacitive materials due to their superior metallic conductivity and thermal stability. Nevertheless, few studies have focused on the origin of pseudocapacitance (Credox) differences for charged molybdenum nitride electrodes with different crystal structures. Herein, taking cubic Mo2N (NaCl-type), Mo3N2 (CsCl-type) and hexagonal MoN (AlB2-type) as the research targets, we have systematically investigated the differences in rate performance and capacitance of these three materials by experimental methods and density functional theory (DFT) calculations to obtain the origin of Credox differences among them. DFT calculations prove that the proportions of Credox are 86.45%, 85.32% and 84.57% for Mo2N, Mo3N2 and MoN and thus the Mo2N features the most obvious pseudocapacitive behavior. Furthermore, the rigid band approximation (RBA) method reveals that the differences of work function change (ΔWF) are the root cause of Credox differences for these three kinds of charged materials. The highest electrochemical capacitance retention, highest conductivity, and fastest K+ ion mobility indicate that the MoN possesses the best rate performance among these three materials. Additionally, the most intact nanowire morphology and smallest ΔWF of Mo2N enable it to possess the highest electrochemical capacitance and theoretical total capacitance (Ctotal). The above findings will shed light on examining capacitance in a charged environment while screening the next-generation high-performance pseudocapacitive materials under various crystal structures.