An improved method based on the Hybrid Finite Element-Statistical Energy Analysis (FE-SEA) method and quasi-steady state theory is proposed to predict the response of spacecraft structure during the process of pyrotechnics separation. Firstly, the amplitude–frequency value of shock load is obtained by using time-frequency conversion technology. Then, according to the frequency response characteristics of each part of the spacecraft structure, a more accurate hybrid FE-SEA model is established. The piecewise loading method is used to predict the response of the hybrid model. Finally, the time domain response results are reconstructed, and the shock response spectrum (SRS) is calculated. Based on the test system of simulating pyroshock, the shock experiment of spacecraft structure is conducted. The high frequency and high velocity character of pyroshock could be effectively simulated, and an accurate shock force function could be obtained through the experiment. This indicates that the numerical results are in line with the ones of the experiment. The SRS obtained from experiments and calculations have similar trends and amplitudes. This conclusion verifies the rationality and sufficient accuracy of the novel method in this paper. The novel method presented in this paper greatly improves the computational efficiency. At the same time, it provides theoretical guidance for shock response prediction of spacecraft structure by steady-state methods.