Abstract Carbon fiber reinforced thermoplastic composites (CFRTP) have garnered increasing attention and are widely utilized in aerospace and other sectors due to their balanced in‐plane mechanical properties. Because of the variety of fabric structures, there is a lack of understanding regarding the correlation between fabric structure and mechanical properties, which hampers the ability to effectively select fabric structures and control the molding process. In this article, four typical bidirectional plain carbon fiber fabrics (CFFs) and polyetheretherketone (PEEK) resin were used as reinforcement materials and matrix, respectively. CFF/PEEK composites with varying CFF structures were prepared using the molding process. The microstructures and mechanical properties of the CFF/PEEK were characterized to investigate the mechanism by which CFF structure influences mechanical properties. The results indicated that the fabric with low areal density and a reduced number of monofilaments exhibited a greater eccentricity in the elliptical cross‐section of fiber yarns. When employed as a reinforcing material, this fabric contributed to enhanced mechanical properties of the CFF/PEEK composites and improved overall structure homogeneity. Furthermore, a mechanical property prediction model for composites with different fabric structures was established, achieving a tensile property prediction accuracy exceeding 90%, which provided a dependable method for selecting other fabric structures. Highlights The microstructures of different CFF/PEEK were quantitatively characterized. The effects of CFF structure on the defects of CFF/PEEK molding were clarified. The relationship between CFF structure and CFF/PEEK properties was established. The influence mechanism on the mechanical properties of the CFF structure was revealed. An accurate prediction model of the tensile properties of CFF/PEEK was established.