Low-lying nuclear states of Sm isotopes are studied in the framework of a collective Hamiltonian based on covariant energy density functional theory. Pairing correlation are treated by both BCS and Bogoliubov methods. It is found that the pairing correlations deduced from relativistic Hartree-Bogoliubov (RHB) calculations are generally stronger than those by relativistic mean-field plus BCS (RMF+BCS) with same pairing force. By simply renormalizing the pairing strength, the diagonal part of the pairing field is changed in such a way that the essential effects of the off-diagonal parts of the pairing field neglected in the RMF+BCS calculations can be recovered, and consequently the low-energy structure is in a good agreement with the predictions of the RHB model.