Rapid identification and quantitative simultaneous analysis for multiple pesticide in real samples based on surface-enhanced Raman spectroscopy (SERS) is still a challenge because of sample complexity, reproducibility, and stability of SERS substrate. With use of colloidal silver nanoparticles loaded three-dimensional (3D) silica photonic microspheres (SPMs) array as the analytical platform, a SERS-based array assay for multiple pesticides was developed in this work. The silver nanoparticles were fixed into the gaps formed by the self-assembled nanospheres of the 3D SPMs to produce "hot spots", on which the Raman enhanced effect was up to 9.86 × 107 and the maximum electric field enhancement effect reached to 9.75 times, ensuring the target pesticides on the surface of the SERS-substrate integrated SPM can be detected sensitively. Using 2,4-dichlorophenoxyacetic acid (2,4-D), glyphosate, and imidacloprid as the testing pesticides, the label-free and high-throughput SERS assay for simultaneous detection of the pesticides was established, giving good linear detection ranges (0.1-204.8 μg/mL for 2,4-D, 0.3-247.9 μg/mL for glyphosate, and 0.2-204.8 μg/mL for imidacloprid) and low detection limits (3.03 ng/mL for 2,4-D, 3.14 ng/mL for glyphosate, and 8.82 ng/mL for imidacloprid). The spiked recovery rates in the real samples were measured in the range of 82-112%, which was consistent with that of the classical standard methods. The label-free 3D SERS array analytical platform provides a powerful tool for high-throughput and low-cost screening of multiple pesticide residues in real samples.