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The 2016 MW7.8 Kaikoura (New Zealand) earthquake was the most complex event ever instrumentally recorded and geologically investigated, as it ruptured on more than 12 fault segments of various geometries. To study the mainshock rupture characteristics, geodetic methods like InSAR and GPS play an essential role in providing satisfactory spatial resolution. However, early strong aftershocks may cause extra ground deformation which bias the mainshock rupture inversion result. In this paper, we will focus on studying the MW 6.3 aftershock, which is the only M6+ thrust slip aftershock that occurred only 30 minutes after the Kaikoura mainshock. We will relocate the hypocenter of this event using the hypo2000 method, make the finite fault model (FFM) inversion for the detailed rupture processes and calculate the synthetic surface displacement to compare with the observed GPS data and figure out its influence on the mainshock study. Although we are not able to resolve the real ruptured fault of this event because of limited observation data, we infer that it is a west-ward dipping event of oblique slip mechanism, consistent with the subfault geometries of the Kaikoura mainshock. According to the inverted FFM, this event can generate 10–20 cm ground surface displacement and affect the ground displacement observation at nearby GPS stations.