In recent years, the study of the crashworthiness of lightweight and efficient thin-walled energy-absorbing structures has received increasing attention. In this work, 3D printing technology was adopted to create a nested origami crash box with stiffness variation, which was made of short carbon fiber reinforced nylon material. The structure effectively inhibits the development of failure behavior of short carbon fiber-reinforced nylon origami crash box due to material brittleness. The quasi-static compression experiment results indicate that compared to origami crash box, nested origami crash box improves by 40% in specific energy absorption and 50% in crash force efficiency, while the initial peak crushing force remains unchanged. The effects of three key geometrical parameters, namely dihedral angle, Distance between tubes, and height difference on the damage mechanism of the NOB are discussed in detail using the finite element method, and the response surface model combined with the non-dominated sorting genetic algorithm II is used for multi-objective optimization. In this work, the concepts of origami theory and nested systems are integrated for the first time, aiming to achieve a stable and efficient energy-absorbing deformation mode by precisely modulating the stress transfer path of the structure and its stiffness. This work provides new ideas for the design and fabrication of novel lightweight energy-absorption boxes.