Mesoporous LiFePO4 (LFP) microspheres embedded homogeneously with three-dimensional (3D) carbon nanotube (CNT) conductive networks were successfully prepared via an effective and controllable hydrothermal approach with the assistance of polyethylene glycol (PEG). Scanning electron microscopy (SEM) and N2 adsorption–desorption characterization demonstrated that porous structure of these microspheres could be well modulated by varying the molecular weight of PEG. The LFP/CNTs composite prepared using PEG400, which possessed the best mesoporous structure with the pore size centered at 40nm, and 3D CNT conductive network embedded in the microspheres homogeneously, exhibited the best electrochemical performance with high capacity retention of 95.7% even at 5C after 100 cycles. Essentially, in comparison with those samples without mesoporous structure or CNT networks, this hybrid microstructure could not only greatly enhance the electrical conductivity, but also facilitate the electrolyte penetration into the microspheres, thus markedly improving the electrochemical performance.