Chemical pesticides have been widely used to increase the yield and quality of agricultural products as they are efficient, effective, and easy to apply. However, the rapid degradation and low utilization ratio of conventional pesticides has led to environmental pollution and resource waste. Nano-sized controlled-release formulations (CRFs) can provide better penetration through the plant cuticle and deliver the active ingredients efficiently to the targeted tissue. In this paper we reported novel conjugated nanospheres derived from 1-naphthylacetic acid (NNA), 3-aminopropyltriethoxysilane (APTES) and tetraethyl orthosilicate and their application as a controlled-release plant growth regulator. The NNA and APTES conjugate was prepared through a covalent cross-linking reaction and subsequent hydrolyzation and polycondensation to synthesize NNA-silica nanospheres. The release data indicated that the release of NNA was by non-Fickian transport and increased as particle size decreased. It was also found that the acidity-alkalinity was enhanced and as the temperature increased, the release of the active ingredient was faster. The nanoconjugate displayed a better efficacy in promoting root formation than NNA technical. The present study provides a novel synthesis route for CRFs comprising a pesticide, with long-duration sustained-release performance and good environmental compatibility. This method may be extended to other pesticides that possess a carboxyl group.