A new variation method is proposed to determine the effective Hamiltonians for conjugated pi-electron systems. This method is based on the minimization of the difference between the ground state reduced single electron density matrix calculated from the effective Hamiltonian and its ab initio counterpart under a set of well-defined constraints. Applications are made to various oligomers of polymethineimine (PMI), polyazine (PAZ) and polyazoethene (PAE) at the Hartree-Fock level. Calculated are also the optical gaps of these oligomers. The effective Hamiltonians contain electron-electron Coulomb interactions and are suitable for the study of excited state dynamic processes such as nonlinear optical properties in pi-conjugated systems.