Abstract: Dynamical analysis of the reactor structure under seismic load is a key procedure during the safety design of the entire reactor system. Due to stochastic and other uncontrollable errors during computation, manufacturing and installation, structural parameters usually subject to a certain amount of uncertainties. Reactor system seismic response influenced by uncertain structural parameters is investigated in this paper. Maximum entropy principle is adopted to construct the probability density distributions (PDFs) of contact stiffness and clearance values among various assemblies of the reactor system. Then, Markov Chain Monte Carlo (MCMC) technique is applied to sample data points according to given PDFs and the input-output data pool is constructed. Distributions of dynamical responses at various locations of the reactor system are examined from the sampled data pool. Results show that the uncertainties near upper and lower core plates depict different distribution patterns. The research in this paper provides a way to quantitatively study the robustness of the seismic analysis and the reliability of dynamical responses in the reactor system.