The strategy of partially substituting cement with carbon-negative biochar to fabricate biochar-cement composites can represent a promising approach to reducing the carbon emissions of the construction industry. However, the detrimental impact on strength development from excessive biochar incorporation remains a significant challenge. To address this issue, this study pioneers a strategy to modify wood waste-derived biochar using seashell waste for enhancing its binding with the cement matrix. Employing a mechanochemical process, the shell-modified biochar was synthesized using oyster shell (OS) and wood waste (WW). The compressive strength of cement composites incorporating 5 wt% modified biochar improved by 3.9–17% compared to the referenced biochar. Even with high biochar incorporation (30 wt%), the compressive strength increased by 58.2% upon modifying the biochar at the OS/WW ratio of 1:9 (10SBC). The modified biochar refined the pore structures, accelerated the hydration kinetics, improved the degree of hydration, and fostered the development of the C-S-H gel network with a longer silicate chain and a higher polymerization degree. Furthermore, the strength enhancement of the biochar-cement composites was attributed to the improved micro-mechanical properties at the interfacial transition zone (ITZ), which increased the volume fraction of high-density C-S-H by 64.4–112% and decreased the low-density C-S-H fraction by 41.8–52.6%. Notably, 10SBC demonstrated a superior improvement due to its cohesive bond with the C-S-H gel and the concurrent densification of C-S-H in the ITZ, which was facilitated by the growth of Ca-/Al-rich hydration products. Overall, this study synergistically upcycled wood and seashell waste into value-added cement additives, thereby achieving strength enhancement of the cement composites.