Aiming at the problem that a large number of material parameters and required for the structural design and numerical simulation of penetration resistance of fiber reinforced composite laminates, this article takes carbon fiber reinforced composite laminates as the research object, and adopts multi-scale simulation method to realize the whole process numerical simulation prediction of micro-, meso-, and macro-scale mechanical properties and penetration resistance of fiber-bundle-laminates. Firstly, microscopic representative volume elements (RVE) were established to predict the mechanical properties of fiber bundles based on the maximum stress criterion. Then, based on Hashin and Hou’s failure criteria, the macroscopic equivalent mechanical properties were predicted by the mesoscopic RVE models established according to the spatial characteristics of braided structures. Finally, an improved Hashin failure criterion considering the strain rate effect was proposed, and the numerical model of ballistic penetration was established based on the literature tests to study the residual velocities and damage characteristics. The results show that the errors of residual velocity results are less than 5%, and the macroscopic numerical models can accurately simulate the damage modes such as fiber fracture as well as interlayer delamination, which verifies the rationality and accuracy of multi-scale simulation method in this article. The relationship between the ballistic limit velocity and the thickness of the plate is linear and the correlation coefficient is above 0.97. The findings of this paper can help to realize the design of low-cost and short-period fiber reinforced composite laminates, which has important scientific and engineering application values for property prediction and inverse structural design of fiber reinforced composite laminates.