Capillary electrophoresis (CE) is well known for its high resolution, rapidity, low sample and reagent consumption, and ability to simply change separation modes, and has been widely used for separation and detection of various analytes important for many fields. One major limitation is the concentration limits of detection, which can be further worsened in complex samples with a significant matrix component. Molecularly imprinted polymers (MIPs) based solid-phase extraction (SPE) and stationary phases (SPs) enjoy great popularity in CE, owing to the recognition specificity, physical robustness, thermal stability, as well as low cost and easy preparation of MIPs. Therefore, herein, recent advances in MIPs-SPE and MIPs-SPs based enrichment and separation for trace analysis in CE are comprehensively reviewed. To the best of our knowledge, this work is the first review covering this topic centered on how MIPs improve CE performance, and provides meaningful advancement over the existing reviews. Three types of approaches to improving CE performance are discussed, including different CE modes, on/off-line molecularly imprinted SPE (MISPE) coupled with CE, and MIPs used as SPs in capillary. Subsequently, typical applications of MISPE and MIPs-SPs for CE determination of a variety of analytes in the fields of food safety, biological medicine and environmental monitoring are summarized. Finally, the possible challenges and perspectives, such as elaborate preparation of MIPs, rational selection of CE modes, pressing development of portable CE devices, are proposed, for promoting CE's detection capability and expanding its real-world applications.