Abstract: Nanopesticides offer unique advantages for the targeted delivery of agrochemicals against destructive plant vascular diseases due to their superior in planta transport capability. However, a fundamental understanding of how nanopesticides penetrate crop tissues and undergo in vivo translocation remains elusive. This knowledge gap severely limits the rational design of targeted nanopesticides and contributes to pesticide waste and ecological contamination. Here, a serine-functionalized polysuccinimide nanocarrier (PSI-Ser) was developed, onto which fludioxonil (Flu) was loaded, yielding Flu-PSI-Ser nanoparticles (NPs) with an average diameter of approximately 80 nm. By comparing the uptake and visualization of Flu-PSI-Ser NPs before and after abscisic acid (ABA) treatment, the nanopesticide can enter the leaf epidermis through stomata. After entering the leaf, the NPs were primarily distributed in the extracellular space, with almost no internalization into the mesophyll cells. During the apoplastic transport of Flu-PSI-Ser NPs, a small fraction of Flu molecules released from the NPs can enter the cytoplasm. Notably, Flu-PSI-Ser NPs demonstrated efficient phloem translocation, allowing systemic movement from treated leaves to underground rhizomes. For a non-systemic fungicide, Flu-PSI-Ser NPs enabled Flu accumulation in rhizome tissues up to 0.601 mg/kg. Owing to their optimized biodistribution and vascular-targeted delivery, Flu-PSI-Ser NPs exhibited approximately 3.2-fold higher control efficacy against banana Fusarium wilt compared with Flu SC concentrate. This study clarifies the tissue-level uptake and long-distance translocation pathways of amino acid-modified nanopesticides in crops, provides a rational delivery strategy for vascular disease management and the development of sustainable agriculture.