Sorption affinity is an essential parameter to immobilize contaminants, but the controlling structures of biochar with strong sorption affinity to organic compounds are unidentified, hindering targeted biochar modification. In the face of multiple types and structures of organic contaminants in the aquatic environment, it is urgent to prepare biochar which can remove a large number of contaminants by targeted biochar modification. This study compared the sorption and desorption of five different type organic contaminants on biochar and graphite to understand sorption affinity and to inform the structural regulation of biochar. The sorption capacity of organics on biochar was 3–7 times higher than graphite, and the desorption ratios of organics on biochar were approximately one-fourth of those on graphite. Hydrophobic areas and aromatic rings were confirmed to be low-energy sorption sites, and most pores were inaccessible. The stronger sorption affinity was thus attributed to the hydrogen bonds between biochar surface functional groups and organics. Furthermore, sorption capacity and desorption ratios correlated positively with calculated sorption thermodynamics and binding energies, aligning with theoretical models based on oxygen- and nitrogen-containing groups. Further verification experiments revealed that functionalized graphite with hydroxyl and carboxyl groups showed the most significantly increased sorption capacity and rate, and decreased desorption ratios, enhancing sorption affinity through hydrogen bonds. These findings offer valuable insights into biochar sorption affinity to organics and guide its structural regulation for organic pollution control in the aquatic environment