Three-dimensional (3D) plasmonic nano-arrays can provide high surface-enhanced Raman scattering (SERS) sensitivity, good spectral uniformity and excellent reproducibility. However, it is still a challenge to develop a simple and efficient method for fabrication of 3D plasmonic nano-arrays with high SERS performance. Here we report a facile approach to construct ordered arrays of silver (Ag) nanoparticles-assembled spherical micro-cavities using polystyrene (PS) sphere template-assisted electrodeposition and post-growth. The electrodeposited small Ag nanoparticles grow into bigger stable nanoparticles during the post-growth process, which could significantly improve the SERS sensitivity. The Ag nanoparticles-assembled 3D micro-cavity array provides much more hotspots in the excitation laser beam-covered volume than the two-dimensional counterpart. The relative standard deviation (RSD) of 612 cm−1 peak of rhodamine 6G (R6G) was calculated to be 8%, and the RSD of the characteristic peak taken from substrates of different batches was less than 10%. The detectable lower concentration as low as 1 fM was achieved for an aqueous solution of R6G. Such SERS substrate also showed high sensitivity to thiram (fungicide) and paraquat (herbicide) in water with limits of detection of 0.067 nM and 2.5 nM respectively. Furthermore, it also demonstrated that SERS detection of pesticide residues on fruits can be realized, showing a potential application in rapid monitoring food safety.