Due to the adjustable structure and the broad application prospects in energy and other fields, the exploration of porous organic materials [metal‐organic polymers (MOPs), covalent organic frameworks (COFs), etc.] has attracted extensive attention. In this work, an imine‐induced metal‐organic and covalent organic coexisting framework (Co−MOP@COF) hybrid was designed based on the combination between the amino units from the organic ligands of Co−MOP and the aldehyde groups from COF. The obtained Co−MOP@COF hybrid with layer‐decorated microsphere morphology exhibited good electrochemical cycling performance (a large reversible capacity of 1020 mAh g−1 after 150 cycles at 100 mA g−1 and a reversible capacity of 396 mAh g−1 at 500 mA g−1) as the anode for Li‐ion batteries. The coexisting framework structure endowed the Co–MOP@COF hybrid with more surface area exposed in the exfoliated COF structure, which provided rapid Li‐ion diffusion, better electrolyte infiltration, and effective activation of functional groups. Therefore, the Co−MOP@COF hybrid material achieved an enhanced Li storage mechanism involving multi‐electron redox reactions, related to the CoII center and organic groups (C=C groups of benzene rings and C=N groups), and furthermore improved electrochemical performance.