Biochar is an affordable and sustainable material for the application of capacitive deionization. Although the desalination capability of biochar is significantly impacted by its pore size distribution, the correlation between them is challenging to explore due to the uncontrollable pore size. This study exclusively utilizes different activation mechanisms to regulate the pore size distribution of carbon derived from the same biomass precursor, and explores the role of pore structures in capacitive deionization. The specific capacitance of microporous biochar (MiB) can reach up to 319.1 F/g (0.2 A/g), with an Epzc of 0.11 V and high oxygen content, while mesoporous biochar (MeB) has a specific capacitance of only 170.4 F/g, an Epzc of 0 V, and a small charge transfer impedance. The MeB//MiB desalination cell is designed based on these characteristics and demonstrates a higher salt adsorption capacity of 17.04 mg/g at 1.2 V, compared to MiB//MiB (15.72 mg/g) and MeB//MeB (6.07 mg/g), alongside a stability of 81 % after 50 cycles. These capabilities can be attributed to the expanded voltage range resulting from the different Epzc, and the high ion storage capacity of MiB, as well as the fast ion transport capability of MeB. The oxygen/carbon ratio of the anode in MeB//MiB increased by only 42 %, whereas that in MiB//MiB increased by 370 %, confirming the oxidation inhabitation ability of the asymmetric structure and the oxidation resistance of MeB. Therefore, constructing ideal pore structures and more importantly reasonable deployment is an effective strategy for improving desalination capacity and stability.