This study aims to develop a novel low-heat cement slurry using phase change microcapsule additives to reduce the decomposition of hydrate-bearing sediments during cementing. Microcapsules were prepared by coating mixed alkanes with polymethyl methacrylate, and lipophilic-modified graphite was incorporated to enhance the thermal conductivity of microcapsules. The effects of microcapsules upon the hydration heat, pore distribution, and compressive strength of the cement slurry/stone were studied through a variety of tests. The results showed that the phase-change temperature, thermal enthalpy, and encapsulation efficiency of the microcapsules were 8.99–16.74 °C, 153.58 Jg−1, and 47.2%, respectively. The introduction of lipophilic-modified graphite reduced the initial phase-change temperature of microcapsules by 0.49 °C, indicating an improvement in their temperature sensitivity. The maximum hydration heat of cement slurry decreased by 41.3% with 7% dosage of microcapsules; the proposed microcapsules outperformed comparable low-heat additives. Moreover, the presence of microcapsules could reduce the number of large pores in (and thereby improve the compressive strength of) cement stone. The innovation of this study is that it comprehensively and intuitively confirms the feasibility of the application of low-heat cement slurry with MPCM as the key in hydrate sediments rather than just focusing on the reduction of hydration heat; furthermore, a self-made cementing device was developed to simulate the cementing process of hydrate deposition. The results show that the thermal regulation of microcapsules inhibited the temperature increase rate of the cement slurry, significantly reducing the damage caused to the hydrate. These findings should improve the safety and quality of cement in offshore oil and gas well applications.