In this paper, we extend the entangled trajectory molecular dynamics (ETMD) method to multidimensional systems. The integrodifferential form of the evolution equation for the Wigner function is employed, allowing general potentials not represented as a polynomial to be treated. As the example, the method is applied to a two-dimensional model of scattering from an Eckart barrier. The results of ETMD are in good agreement with quantum hydrodynamics and exact quantum simulations. By comparing the quantum and classical trajectory in phase space, the quantum tunneling phenomenon is interpreted vividly.