Optimal control of a class of hybrid dynamical systems is studied using the method of dynamic programming. It is proved that the value function is a discontinuous viscosity solution of the corresponding Hamilton-Jacobi-Bellman (HJB) equation which appears as a system of quasi-variational inequalities (SQVI) coupled by a nonlocal operator with a variable boundary condition. The comparison theorems are established for the sub- and super-solutions of the SQVI.