Nanopesticides have received increasing attention in modern agricultural production. Before large-scale application, it is necessary to evaluate the environmental risks and safety of nanopesticides. Different pesticides are encapsulated into different nanomaterials, which have varying effects on the growth and metabolism of different non-target crops. In this work, a novel acid-responsive nanoparticles (Nps) coating the fungicide boscalid (Bos) based on the metal-organic framework material zeolitic imidazolate framework-8 (ZIF-8) was constructed (Bos@ZIF-8). Nps had good slow-release performance and fungicidal activity against Rhizoctonia solani (R. solani). The growth and metabolic regulation of rice seedlings after treatment with Bos@ZIF-8 Nps were investigated. The height and the root length of rice seedlings were measured. Metabolites, including saccharides, amino acids, organic acids, flavonoids, and various functional enzymes, were analyzed. Bos@ZIF-8 Nps, especially at low and medium concentrations, exhibited a positive trend in regulating crop growth and metabolism, and offset the partial negative effects of Bos due to the introduction of zinc ions. This work provides a reference for the large-scale application of nanopesticides in agricultural production.