A tidal lagoon system has multiple environmental, societal, and economic implications. To investigate the mechanism of influence of the geomorphological evolution of a tidal lagoon, the effect of critical erosion shear stress, critical deposition shear stress, sediment settling velocity, and initial bed elevation were assessed by applying the MIKE hydro- and morpho-dynamic model to a typical tidal lagoon, Qilihai Lagoon. According to the simulation results, without sediment supply, an increase of critical erosion, deposition shear stress, or sediment settling velocity gives rise to tidal networks with a stable terrain. Such an equilibrium state can be defined as when the change of net erosion has little variation, which can be achieved due to counter actions between the erosion and deposition effect. Moreover, the influence of the initial bed elevation depends on the lowest tidal level. When the initial bed elevation is below the lowest tidal level, the tidal networks tend to be fully developed. A Spearman correlation analysis indicated that the geomorphological evolution is more sensitive to critical erosion or deposition shear stress than sediment settling velocity and initial bed elevation. Exponential sea level rise contributes to more intensive erosion than the linear or the parabolic sea level rise in the long-term evolution of a tidal lagoon.