To address the high costs associated with the manufacturing, transportation, and offshore installation of large and complex artificial reefs, and to meet the demand for low-cost and highly stable reef structures in deep-sea marine ranching, a novel design concept in which small reef units are freely stacked to form a large-scale reef was proposed. Specifically, multiple small-scale reef units, designed for easy interlocking, are randomly deployed and accumulated to form a stable large reef structure. This approach reduces the requirements for deployment equipment and installation complexity, thereby enabling cost-effective reef construction in deep offshore environments. The formation of large reef structures through the random stacking of small units requires careful design of the unit geometry, deployment quantity, and overall structural stability. Therefore, the discrete element method (DEM) was employed to numerically simulate the deployment and stacking process, investigating the interaction forces between reef units and their accumulation behavior. By comparing geometric parameters of the resulting reef mound, such as spatial growth rate, stacking height, base area, and slope, the interlocking performance of the reef structure was analyzed, and the unit geometry was further optimized. In addition, shaking table experiments were conducted to validate the stability of the stacked reef structure. The results demonstrate that the DEM model can effectively reproduce the stacking process of small reef units, and that optimization of unit geometry can be achieved through comparative analysis of reef mound parameters. The self-stacking reef units exhibit rapid accumulation and stable interlocking, ultimately forming a large-scale reef structure with a favorable spatial configuration and mechanical stability. This study provides a new technical pathway for the low-cost construction and large-scale application of artificial reefs in deep offshore environments.