Assessing agrochemical residues is crucial for food safety and consumer health. Surface-assisted laser desorption/ionization mass spectrometry (SALDI-MS) has been proven to be efficient for pesticide detection, however its uneven substrate surface distribution limits its practical applicability. Improving detection sensitivity while maintaining detection repeatability is still challenging. In this study, a 3-D heterostructure integrated pyramid silicon and zinc oxide nanorods (pyramid Si-ZnO NRs) was proposed as a SALDI-MS substrate to enhance detection sensitivity and repeatability. The pyramid Si-ZnO NRs improve light trapping and hole-electron separation efficiency, significantly boosting SALDI-MS sensitivity. The limit of detections (LODs) for thiabendazole, imidacloprid, and berberine in beverages are respectively as low as 0.45 nM, 0.17 nM and 81 pM. The superhydrophobic substrate suppresses the "sweet spot" effect, improving repeatability with relative standard deviations (RSDs) under 10 %. This platform is a sensitive, reliable tool for detecting pesticide residues, with potential applications in food safety.