The low-frequency (LF) oscillations inside an elongated rectangular harbor near the offshore fringing reef excited by bi-chromatic short wave groups are simulated using a fully nonlinear Boussinesq model. Based on a LF wave analysis procedure, effects of reef-face slope and reef ridge on the maximum LF wave amplitude, the free and the bound LF waves and their relative components inside the harbor are investigated systematically under the conditions of the 2nd to the 5th modes and wave breaking occurring over the reef. Results show that the variation trends of the maximum LF wave amplitude and the free LF wave amplitude with respect to the reef-face slope are almost identical with each other for all the four modes studied in this paper, no matter whether the reef ridge exists or not. For the 4th and 5th modes, the reef ridge has obvious influences on the LF waves inside the harbor. Under these two modes, the existence of the reef ridge always decreases the bound LF wave amplitude and its ratio to the free LF wave amplitude inside the harbor, while its influences on the maximum LF wave amplitude and the free LF wave amplitude both depend on the reef-face slope.