In this work, the mechanical and dynamic thermomechanical properties of PEEK based on FDM are experimentally investigated and evaluated comprehensively. The tensile failure mechanism of PEEK prepared by FDM and extrusion modeling (EM) was analyzed by fracture morphology observation. By conducting a differential scanning calorimetry (DSC) test, the crystallinity of PEEK prepared by FDM and EM was measured. The dynamic thermomechanical properties of PEEK were tested and analyzed by dynamic mechanical analysis (DMA). For FDM-prepared PEEK samples, the yield strength and elongation were 98.3 ± 0.49 MPa and 22.86 ± 2.12%, respectively. Compared with the yield strength of PEEK prepared by EM, the yield strength of PEEK prepared by FDM increased by 65.38%. The crystallinity of FDM-prepared and EM-prepared samples was calculated as 34.81% and 31.55%, respectively. Different processing methods resulted in differences in the microscopic morphology and crystallinity of two types of PEEK parts, leading to differences in mechanical properties. The internal micropores generated during the FDM processing of PEEK significantly reduced the elongation. Moreover, according to the DMA results, the glass transition activation energy of PEEK was obtained as ΔE = 685.07 kJ/mol based on the Arrhenius equation. Due to the excellent mechanical properties of PEEK prepared by FDM processing, it is promising for high-performance polymer applications in different fields.