We present a source inversion of the 2008 Wenchuan, China earthquake, using strong-motion waveforms and geodetic offsets together with three-dimensional synthetic ground motions. We applied the linear multiple time window technique considering geodetic and dynamic Green's functions computed with the finite element method and the reciprocity and Strain Green’s Tensor formalism. All ground motion estimates, valid up to 1 Hz, accounted for three-dimensional effects, including the topography and the geometry of the Beichuan and Pengguan faults. Our joint inversion has a higher moment (M0) than a purely geodetic inversion and the slip distribution presents differences when compared to one-dimensional model source inversions. The moment is estimated to be M0=1.2x1021 Nm, slightly larger than other works. Our results show that considering a complex 3D structure reduces the size of large areas of 10 m slip or greater by distributing it in wider zones, with reduced slips, in the central portion of the Beichuan and the Pengguan faults. Finally, we compare our source with a relocated aftershock catalog and conclude that the 4-5 m slip contours approximately bound the absence or presence of aftershocks.