We inverted the high-resolution spatiotemporal slip distribution of the 21 September 1999 Chi-Chi, Taiwan, earthquake utilizing data from densely distributed island-wide strong motion stations for a three-dimensional (3-D) fault geometry, and 3-D Green's functions calculations based upon parallel nonnegative least squares inversion. The 3-D fault geometry, consistent with high-resolution reflection profile, is determined from GPS inversion and aftershocks distribution. This 3-D fault model presents the dip angle gradually becoming shallower from south to north along the fault and near flat at the deeper portion of the fault. The 3-D Green's functions are calculated through numerical wavefield simulation from three-dimensional heterogeneous velocity structure derived from tomography studies. The Green's functions show significant azimuthal variations and suggest the necessity of lateral heterogeneity in velocity structure. Considering complex fault geometry and Green's functions in full 3-D scale, we invert the spatial/temporal slip distribution of the 1999 Chi-Chi earthquake using the best available and most densely populated strong motion waveform data. We perform the inversion under a parallel environment utilizing multiple-time window to manage the large data volume and source parameters. Results indicate that most slip occurred at the shallower portion of the fault above the decollement. Two major asperities are found, one in the middle of the fault and another one at the northern portion of the fault near the bend in the fault trace. The slip in the southern portion of the fault shows a relatively low slip rate with longer time duration, while the slip in the northern portion of the fault shows a large slip rate with shorter time duration. The synthetics explain the observations well for the island-wide distributed strong motion stations. This comprehensive study emphasizes the importance of realistic fault geometry, 3-D Green's functions, and parallel inversion technique in correctly accounting for both the detailed source rupture process and its relationship with the strong ground motion of this intense earthquake.