Herein, a new generic fiber array based on molecular imprinting solid-phase microextraction (MIP-SPME) technology, was described to enrich trace multiple neonicotinoids with high flux from the food matrix. To begin with adsorption experiments coupled with theoretical calculations provided universal means for selecting the preferred template molecule clothianidin (CLT). Results demonstrated that the CLT-MIP fiber array exhibited significantly superior enrichment ability of 1189–2356-folds for six neonicotinoids compared with two kinds of commercial fiber arrays. Furthermore, the practicability of the CLT-MIP fiber array was verified by simultaneously determining multiple neonicotinoids in tea and honey samples. The CLT-MIP fiber array showed a limit of detection (LOD) of 0.03–0.58 μg/L for six neonicotinoids. The method also exhibited satisfactory recoveries ranging from 85.4% to 116.8% with RSD (n = 3) less than 8.8%. The imprinted fiber array has the advantages of high-throughput, predominant reproducibility, and accurate quantitation multi-component, and it may open up a new mean to efficiently enrich high-throughput and simultaneously detect multiple compounds from food samples.