Despite being one of the most promising materials in anode materials, molybdenum sulfide (MoS2) encounters certain obstacles, such as inadequate cycle stability, low conductivity, and unsatisfactory charge‐discharge (CD) rate performance. In this study, a novel approach is employed to address the drawbacks of MoS2. Carbon polymer dots (CPDs) are incorporated to prepare three‐dimensional (3D) nanoflower‐like spheres of MoS2@CPDs through the self‐assembly of MoS2 2D nanosheets, followed by annealing at 700 °C. The CPDs play a main role in the creation of the nanoflower‐like spheres and also mitigate the MoS2 nanosheet limitations. The nanoflower‐like spheres minimize volume changes during cycling and improve the rate performance, leading to exceptional rate performance and cycling stability in both Lithium‐ion and Sodium‐ion batteries (LIBs and SIBs). The optimized MoS2@CPDs‐2 electrode achieves a superb capacity of 583.4 mA h g−1 at high current density (5 A g−1) after 1000 cycles in LIBs, and the capacity remaining of 302.8 mA h g−1 after 500 cycles at 5 A g−1 in SIBs. Additionally, the full cell of LIBs/SIBs exhibits high capacity and good cycling stability, demonstrating its potential for practical application in fast‐charging and high‐energy storage.