Transverse compression-induced cross-sectional deformation of parallel fiber bundles usually acts as the fundamental structural mechanism for bundle-based materials. In the present article, a meso-scale insight into the cross-sectional responses of parallel fiber bundle under transverse compression was made. A novel algorithm was proposed to design and model the bundle cross-sectional meso-structure with randomly distributed fibers. The transverse compression induced bundle cross-sectional responses (including cross-sectional perimeter, area and filling factor) were simulated and analyzed based on the finite element method, and were verified experimentally for the bundle with 91 fibers. Results showed that the load began to increase significantly when the perimeter growth rate of the bundle cross-section was larger than 0.8, and the load gradually reached the peak value when the perimeter growth rate was about 1.5. The Mises stress distribution of the bundle gradually neared to the Gaussian distribution when load sharply increased. The results presented in the current paper can provide a novel method to generate randomly distributed fibers and a theoretical guidance for the mechanical properties prediction of bundle-based materials by analyzing the bundle cross-sectional deformation in transverse compression.