We investigate quantum dynamics in a double-well system subject to time-dependent perturbation with some incommensurate frequencies using entangled trajectory molecular dynamics method. We first compare time evolution of energy of the driven system with two mode perturbation under classical dynamics with one under quantum dynamics, it is found that quantum dynamics obeys Ehrenfest's theorem and it shows our results obtain from entangled trajectory molecular dynamics method are correct and accurate. Quantum coherence suppresses trajectory which initial energy is higher than barrier to get over it, this process is named coherent destruction of tunneling (CDT). We show this interesting phenomenon through showing entangled trajectory and corresponding classical trajectory in phase space and discuss their energy fluctuation with time. Furthermore, we discuss quantum dynamics with different frequency mode perturbation from the perspective of autocorrelation evolution, classical chaos brings remarkable influence on quantum-mechanical phenomena.