The work aims to study the strongly heterogeneous three-dimensional packing problem with interlayer cushion, realize the rapid calculation of the packing and the cushion scheme of the capsule box to instruct the packing, so as to improve the packing rate and efficiency of the capsule box, this work. Based on the actual packing requirements of the capsule box, a two-step optimization heuristic algorithm based on greedy strategy and improved packing sequence strategy was designed to optimize the packing and cushion scheme with the goal of minimizing the volume of the cushion. And according to different placement directions, different output results were designed to instruct packing. Compared with the data before packing optimization, the experimental results showed that the packing scheme and the cushion scheme recommended by this algorithm could reduce the number and volume of wooden cases, reduce the volume of cushion by 7.21%, and save about half the packing time. The hybrid heuristic algorithm designed in this paper can find the optimal packing and cushion scheme for the capsule box packing problem, reduce the use of cushion, and improve the packing rate and efficiency.