It remains challenging to develop a techno-economically feasible method to remove alkali and alkaline earth metal species (AAEMs) from rice husk (RH), which is a widely available bioresource across the world. In this study, the AAEMs leaching effect of aqueous phases of both bio-crude prepared by hydrothermal liquefaction (AP-HT) and bio-oil prepared by pyrolysis (AP-Pyro) of RH were systematically investigated. The results indicated that although the acidity of AP-HT and AP-Pyro are much lower than that of HCl, they performed a comparable removal efficiency on AAEMs (Na: 56.2%, K: 96.7%, Mg: 91.0%, Ca: 46.1% for AP-HT, while Na: 58.9%, K: 96.9%, Mg: 94.0%, Ca: 86.3% for AP-Pyro) with HCl. The presence of phenolics in bio-oil could facilitate the penetration of water and organic acids into the inner area of RH cells, thus enhancing the AAEMs removal via chelate reactions. The thermal stability of leached RH during thermochemical conversions was studied via TG and Py-GC-MS. The results showed that the heat conduction efficiency in leached RH was enhanced with a high pyrolysis rate, resulting in a narrow carbon chain distribution (C5−C10) of derived chemical compounds.