The rational construction of Ti3C2Tx MXene‐based composites has been deemed as a popular way to improve their electrochemical energy storage performances owing to the unique two‐dimensional (2D) structure, excellent conductivity, and good flexibility. However, it remains a major challenge to assemble mesoporous carbon onto Ti3C2Tx with fewer oxygen‐containing groups by using surfactants with short hydrophilic segments. In the work, we propose a molecular engineering assembly strategy for the growth of N,P co‐doped mesoporous carbon onto Ti3C2Tx nanosheets (NPMC/Ti3C2Tx) under the assistance of phytic acid by using melamine‐formaldehyde resin and pluronic P123 (PEO20PPO70PEO20) as the carbon/nitrogen source and soft template, respectively. The detailed investigations reveal that phytic acid with abundant hydroxyl groups can effectively enhance the hydrogen bond interactions among P123, carbon precursor, and Ti3C2Tx nanosheets, thus ensuring the efficient assembly of mesoporous carbon onto Ti3C2Tx. The obtained NPMC/Ti3C2Tx composite demonstrates a set of merits, including cylindrical mesopore, N,P co‐doping, and a good combination of mesoporous carbon and Ti3C2Tx nanosheets. As a result, it exhibits an improved lithium‐ion storage performance, delivering a high reversible capacity of 556.3 mA h g−1 after 100 cycles at 0.1 A g−1. The present work provides a feasible molecular engineering assembly route for the rational design of high‐performance Ti3C2Tx MXene‐based electrodes.