To improve the setting time and mechanical performance of magnesium phosphate cement (MPC), MPC was modified with metakaolin at different replacement dosages. Setting time, compressive strength, and flexural strength were measured, and the underlying mechanisms were examined in conjunction with pore-structure characteristics and microstructural analyses. The results show that metakaolin effectively prolongs the setting time of MPC; at a dosage of 40%, the setting time increased to 34 min. An appropriate amount of metakaolin markedly enhances both early-age and later-age mechanical properties, with 30% identified as the optimal dosage, yielding 28 d compressive and flexural strengths of 58.48 MPa and 10.15 MPa, respectively. Metakaolin significantly reduces the porosity of MPC and refines the pore size distribution. The fractal dimension of harmful pores can serve as an important indicator for evaluating pore-structure optimization and strength evolution. Metakaolin also promotes the formation of MgKPO4·6H2O and AlH3(PO4)2·H2O, and improves the mechanical properties and microstructure of MPC through filler effects, nucleation effects, and its reactive activity.