A crystal with ion pre-intercalation structure has advantage that benefits electrolyte ion intercalation/deintercalation and less deformation in structure. However, the capacitance loss in long time cycles is still a problem in some ion pre-intercalation materials. To improve cycle lifetime of supercapacitor, new electrode materials with fast redox reactions and high stability are highly desired, and the ion diffusion behaviors in the crystal during the charge/discharge process should be understand. Herein, we report a new type electrode material, Na2Mn8O16 nanorods with Na ion pre-intercalation in tunnel structure, which exhibits excellent performance for supercapacitor. The Na2Mn8O16 electrode achieves capacitance 744.8, 738.2 and 667.5 F/g under the current density of 1 A/g in Li2SO4, Na2SO4 and K2SO4 aqueous electrolytes, respectively, which also show long cycle life with 93.5%, 96.1% and 91.1% capacitance retention after 10,000 cycles. Atomic-scale ion diffusion behaviors in the tunnel-structure of Na2Mn8O16 are studied by the density functional theory calculation. The experimental and theoretical investigations together unveil that both redox reaction and ion intercalation in tunnel structure contribute to the high capacitance and long cycle life in various neutral sulfate electrolytes. In addition, symmetric all-solid-state flexible supercapacitors based on the Na2Mn8O16 electrodes demonstrate practical applications in electrochemical energy storage.