Based on the explicit FE method and parallel computing cluster platform of ABAQUS, a large-scale refined two-dimensional (2D) nonlinear FE model is developed in the time domain with considering the heterogeneity of ground soils, for a typical site on the estuarine basin with undulating bedrock and nonuniformly distributed soil layers. The artificial viscoelastic boundary condition is proposed for simulating the semi-infinite field, the main characteristics of basin surface ground motion are analyzed, including the motion amplitude, spectrum, duration and transfer functions, and the accumulation effect of ground motion and edge effect of basin are investigated. The results show that: (1) The amplification effect at different observation points on the basin ground surface is observed; and the peak ground acceleration(PGA)of basin ground surface displays a non-monotonic decrease with soil depth; the prominent accumulation effect is found to be at particular positions where the bedrock surface sharply undulates, and the pronounced edge effect is found to be on both sides of basin; the moderate and long-period ground motions of the basin are significantly amplified compared to the short-period motions. (2) For the earthquakes with high, moderate and low occurrence probabilities, the predominant periods of the basin are 0.35-0.65 s, 0.40-0.75 s and 0.50-1.05 s, respectively；the mean value contours of the peak ground acceleration and site predominant periods of the basin are plotted, and the recommended values of the amplification factor of ground motion acceleration response spectra for different period intervals are given. The seismic effect coefficient amax and characteristic period Tg of the design parameters of ground motion by this paper are significantly larger than those of the Chinese code for seismic design of buildings. (3) Ground motion durations at different points of basin ground surface extend over several orders, and the duration is also closely related to the bedrock motion characteristics. (4) Amplification effect and accumulating effect of the basin ground motion are more significant for the frequency band from 0.5 Hz to 2 Hz; while for the frequency band lower than 0.2 Hz or higher than 2.5 Hz, the ground motion amplification characteristics are insignificant. (5) Ground motion amplification effects in Fuzhou city downtown area and its adjacent areas of the basin are generally larger, compared to other areas. It is indicated that the large-scale two-dimensional nonlinear FE model can describe the influence of micro topographic relief and nonuniformly distributed basin soil layers on seismic wave propagation.