For a clustered launch vehicle with extremely complex elastic characteristic, serious chattering of elastic mode occurs in the continuous variable coefficient time domain simulation of its control system. In this paper, the reason of chattering is pointed, and some technologies such as normalization of the elastic mode based on their characteristics, and improvement on the interpolation algorithm are provided. The validity of these technologies is proved by theoretical analysis and mathematical simulation. For a kind of complex structure dynamics and control coupling system, these methods can be effectively used to resolve the chattering phenomena in its mathematical simulation, and can be generalized in the control system design of large and complex spacecraft.