We calculate one-loop renormalization factors of three-quark operators, which appear in the low energy effective Lagrangian of the nucleon decay, for $O(a)$-improved quark action and gauge action including six-link loops. This calculation is required to predict the hadronic nucleon decay matrix elements in the continuum regularization scheme using lattice QCD. We present detailed numerical results of the one-loop coefficients for general values of the clover coefficients employing the several improved gauge actions in the Symanzik approach and in the Wilsons renormalization group approach. The magnitudes of the one-loop coefficients for the improved gauge actions show sizable reduction compared to those for the plaquette action.