The longitudinal compressive properties of carbon fiber/nanoparticles reinforced polymer unidirectional composites are investigated by experiments and a series of numerical simulations based on fast Fourier transforms (FFT) method taking into consideration matrix plastic behavior and initial fiber waviness. The efficient and accurate FFT-based method is convenient and has the low computation cost to discuss the effects of material and geometric parameters on the longitudinal compressive strength in details. The proper filling nanoparticles can significantly increase the longitudinal compressive strength. The computational results for failure mechanisms and strength show a good consistency with our experimental results. The present study provides reliable guidance for designing the fiber reinforced polymer composites with better damage tolerance.