Influences of topographic variations of the offshore fringing reef on the harbor oscillations excited by incident N-waves with different amplitudes and waveform types are studied for the first time. Both the propagation of the N-waves over the reef and the subsequently-induced harbor oscillations are simulated by a Boussinesq-type numerical model, FUNWAVE-TVD. The present study concentrates on revealing the influences of the plane reef-face slope, the reef-face profile shape and the lagoon width on the maximum runup, the wave energy distribution and the total wave energy within the harbor. It shows that both the wave energy distribution uniformity and the total wave energy gradually increase with decreasing reef-face slope. The profile shape of the reef face suffering leading-elevation N-waves (LEN waves) has a negligible impact on the wave energy distribution uniformity, while for leading-depression N-waves (LDN waves), the latter gradually decreases with the mean water depth over the reef face. The total wave energy always first increases and then decreases with the mean water depth over the reef face. In general, the total wave energy first sharply decreases and then slightly increases with the lagoon width, regardless of the reef-face width and the incident waveform type. The maximum runup subjected to the LEN waves decreases monotonously with the lagoon width. However, for the LDN waves, its changing trend with the lagoon width relies on the incident wave amplitude.