The 2007 Mw 6.6 Niigata‐ken Chuetsu‐Oki earthquake implies a complex fault mechanism. Several surveys suggest the possibility of two main segments crosscutting each other at their center (i.e., a northern segment dipping to the northwest and a southern segment dipping to the southeast). We modeled the dynamic rupture propagation numerically along the inferred segmented fault system using a boundary integral equation method (BIEM). The possibility of rupture transfer is numerically demonstrated, and two rupture modes are described. Simultaneous rupture transfer along the overlapping part is possible only under a high‐stress load; however, this rupture mode yields an excessively high slip value. Otherwise, where regional stress is relatively low but pore pressure is high enough to govern the rupture criterion (described as the low frictional coefficient case in this study), the rupture transfer to the other segment does not occur until rupture terminates on the first segment regardless of the crosscutting distance between the two segments. In this case, at the central crosscutting part, a possible rupture scenario is that ruptures occur sequentially in different directions: first a southbound rupture on the northwest‐dipping segment, then a northbound rupture triggered on the southeast‐dipping segment a few seconds later. The simulated rupture scenario on crosscutting faults can be strongly influenced by a preexisting fault structure determined by Miocene rifting during an opening stage of the Sea of Japan and the subsequent shortening of the crust. Our results point to the importance of investigating earthquake rupture scenarios in complex fault systems based on existing geophysical and geological information and dynamic rupture mechanics.