Abstract: This study employed metalaxyl-M and fludioxonil as the active ingredients of fungicides, and selected cost-effective and readily producible nano-calcium carbonate and attapulgite as carrier materials to develop a controlled-release fungicide system. First, fludioxonil@nano-calcium carbonate system with a core-shell structure was prepared. Then, it was mixed with metalaxyl-M technical, and attapulgite was used as the carrier to construct a fludioxonil@nano-calcium carbonate@metalaxyl-M/attapulgite system with a double-layer core-shell structure. Subsequently, the morphology, crystal structure, thermal stability, particle strength, and release behavior of the proposed pesticide-loaded system were characterized and optimized. Eventually, a stable granular pesticide-loaded system with good release performance was obtained (the mass fraction of fludioxonil and metalaxyl-M was 0.04% and 0.06%, respectively). fludioxonil was successfully loaded into the nano-calcium carbonate carrier, achieving a maximum loading rate of 43.39%. Its release pattern followed the first-order kinetic model (R² = 0.9237), and the particle strength was (6.97 ± 0.74) MPa, meeting the sowing strength requirements of traditional granules. Field trials employing the "simultaneous pesticide and seed sowing" method demonstrated that, compared with conventional seed coatings, this pesticide-loaded system could markly improve the seedling emergence of soybean (increasing from 87.6% to 91.8%–99.9%) and reduce the disease index of soybean root rot (decreasing from 14.4 to 4.7-6.9), with no phytotoxicity observed in soybean plants. This study provides a new technical approach for the efficient prevention and control of soybean root rot and offers theoretical guidance for the refined design of controlled-release pesticide formulations.