A novel phase change microcapsule has been developed and synthesized for solar energy storage systems. The fabrication process involved the in-situ polymerization of phase change microcapsules, wherein cellulose nanocrystals (CNCs) were employed as Pickering emulsifiers and nano-fillers to enhance the properties of the melamine formaldehyde resin (MF) shells. These enhancements included improved emulsifying ability, mechanical strength, and sustainability. Subsequently, black phosphorus (BP), a two-dimensional material with high solar absorption intensity and a wide frequency range, was covalently modified by MF to enhance the photothermal capacity of the microcapsules and reduce the thermal resistance between the photothermal material and the phase change material (PCM), this functionalized BP was referred to as MF@BP. The phase change microcapsules without and with MF@BP exhibit high latent heat values of 210.79 J g−1 and 207.92 J g−1, respectively. Furthermore, the PCM core content was measured at 88.9% and 88.5%, and the encapsulation rates are 99.0% and 98.8%, respectively. The PCM microcapsules with MF@BP demonstrated excellent photothermal characteristics with an efficiency of 92.04%. Additionally, the PCM microcapsules exhibit stability below 200 °C and retain 99.4% of their latent heat even after 100 cycles of heating and cooling. Furthermore, the PCM microcapsules display self-extinguishing properties due to the flame retardancy of the MF shell, and the incorporation of black phosphorus further enhanced the flame retardancy. Overall, these PCM microcapsules exhibit significant potential for utilization in solar energy systems.