To explore the influence of the crystal structure difference of melamine trimetaphosphate (MAP) on the application performance of its polymer composites, an intumescent flame retardant with the optimal crystal type was designed and synthesized to improve the mechanical properties and flame retardancy of polyamide 6 (PA6). I-MAP and II-MAP were obtained using different concentrations of MA and sodium trimetaphosphate (STMP) in an acidic aqueous solution. The morphology, chemical composition, and thermal stability were comprehensively characterized by Fourier transform infrared (FTIR) spectroscopy, X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), X-ray diffraction (XRD), and thermogravimetric analysis (TGA). The dispersion, mechanical properties, and flame retardancy of PA6/I-MAP and PA6/II-MAP were evaluated by SEM, stress and strain, limiting oxygen index test (LOI), vertical burning test (UL-94), cone calorimetry (CONE) test, and char residue analysis. The conclusion is as follows: I-MAP and II-MAP have a greater influence on the physical properties of PA6 but less influence on the chemical properties. Compared with PA6/I-MAP, the tensile strength of PA6/II-MAP is 104.7% higher, the flame rating reaches V-0, and PHRR is reduced by 11.2%.