Anomalous diffusions are ubiquitous in nature, whose functional distributions are governed by the backward Feynman-Kac equation. In this paper, the local discontinuous Galerkin (LDG) method is used to solve the 2D backward Feynman-Kac equation in a rectangular domain. The spatial semi-discrete LDG scheme of the equivalent form (obtained by Laplace transform) of the original equation is established. After discussing the properties of the fractional substantial calculus, the stability and optimal convergence rates of the semi-discrete scheme are proved by choosing an appropriate generalized numerical flux. The $L1$ scheme on the graded meshes is used to deal with the weak singularity of the solution near the initial time. Based on the theoretical results of a semi-discrete scheme, we investigate the stability and convergence of the fully discrete scheme, which shows the optimal convergence rates. Numerical experiments are carried out to show the efficiency and accuracy of the proposed scheme. In addition, we also verify the effect of the central numerical flux on the convergence rates and the condition number of the coefficient matrix.