An algorithm to construct the generator of gauge transformation for a system with singular higher-order Lagranian in field theories is given. Starting from generating functional of Green function in phase space, the Ward identities in canonical formalism for the constrained Hamiltonian system are deduced. It is pointed out that the quantal canonical equation for such a system deffers from the classical canonical equation, arising from the fact that Dirac conjecture is valid. The quantization for a generalized dynamical system which can be equivalent to Chern-Simons theory is given. With preliminary application of canonical Ward identities to such a system, some relationships among the vertices and propagators for the fields can be deduced without carrying out the integration for canonical momenta in phase space path integral.