The highly water-soluble nematicide fosthiazate is anticipated to undergo microencapsulation in order to enhance its retention around plant roots and mitigate leaching into groundwater. However, the underlying mechanism governing the influence of hydrophilicity of the microcapsule (MC) core on the evolution of the microcapsule shell remains unclear, posing challenges for encapsulating water-soluble core materials. This study elucidates the microlevel formation mechanism of microcapsules by investigating the impact of interfacial mass transfer on shell formation and proposes a method for regulating the structure of shells. The study reveals that enhancing the hydrophilicity of the core enhances the shuttle effect between the oil and aqueous phase, expands the region of polymerization reactions, and forms a loose and thick shell. The thickness of the microcapsule shell prepared using solvent oil 150# (MCs-SOL) measures only 264 nm, while that of the microcapsules prepared using propylene glycol diacetate and solvent oil 150# at a ratio of 2:1 (MCs-P2S1) is 5.2 times greater. The enhanced compactness of the shell reduced the release rate of microcapsules and the leaching distance of fosthiazate in soil, thereby mitigating the risk of leaching loss and facilitating the distribution of active ingredients within crop roots. The MCs-SOL had a limited leaching distance measurement of 8 cm and exhibited a satisfactory efficacy of 87.3% in controlling root galling nematodes. The thickness and compactness of the MCs shell can be regulated by manipulating the interfacial shuttle effect, providing a promising approach to enhancing utilization efficiency while mitigating potential environmental risks.