The conversion of waste biomass into biochar through inert pyrolysis represents a promising strategy for carbon sequestration. However, biochar production is often accompanied by the release of small molecular chemical substances during pyrolysis, and the resulting biochar is susceptible to environmental degradation. To enhance the carbon retention rate of biochar during pyrolysis and its stability in the environment, this study explored the incorporation of various metal soluble salts (CaCl₂, Ca(H₂PO₄)₂, MgCl₂, FeCl₃) and clay minerals (quartz, goethite, bentonite, albite) with two types of waste biomass (phragmites and goldenrod) for pre-treatment to enhance both carbon retention and stability in the resulting biochar. Furthermore, to elucidate the regulatory mechanisms of minerals on biochar structural formation, the three primary components of raw biomass—hemicellulose, cellulose, and lignin—were individually mixed with the minerals at a ratio of 1:5 (mineral/biomass, w/w) to produce biochars for a comparative analysis. The experimental results demonstrated that metal soluble salts, particularly Ca(H₂PO₄)₂, exhibited a superior performance in enhancing biochar’s carbon retention compared to clay minerals. Specifically, Ca(H₂PO₄)₂ treatment resulted in a remarkable 15% increase in the carbon retention rate. Through K₂Cr₂O₇ oxidation simulating soil aging conditions, Ca(H₂PO₄)₂-treated biochar showed approximately 12% greater stability than the untreated samples. This enhanced stability was primarily attributed to the formation of stable chemical bonds (C–O–P and P–O), which facilitated the preservation of aromatic carbon structures and small molecular compounds including sugars, alcohols, and ethers. Mechanistic investigations revealed that Ca(H₂PO₄)₂ significantly influenced the pyrolysis process by increasing the activation energy from 85.9 kJ mol⁻¹ to 156.5 kJ mol⁻¹ and introducing greater reaction complexity. During the initial pyrolysis stage (<300 °C), Ca(H₂PO₄)₂ catalyzed depolymerization, ring-opening, and C–C bond cleavage in hemicellulose, enhanced cellulose depolymerization, and side-chain cleavage in lignin phenylpropanes. In the intermediate temperature range (300–400 °C), Ca(H₂PO₄)₂ facilitated carboxylate nucleophilic addition reactions and promoted cyclization to form aromatic carbon structures. The innovative aspect of this work is that minerals can increase both the yield and carbon retention rate of biochar. Furthermore, it reveals the mechanisms underlying the improvements in pyrolysis, providing a scientific basis and theoretical foundation for better displaying the carbon sequestration potential of biochar in future applications.