A pixel structure and a manufacturing method thereof are provided. The pixel structure includes a substrate, a scan line, a data line, a first insulating layer, an active device, a second insulating layer, a common electrode and a first pixel electrode. The data line crossed to the scan line is disposed on the substrate and includes a linear transmitting part and a cross-line transmitting part. The first insulating layer covering the scan line and the linear transmitting part is disposed between the scan line and the cross-line transmitting part. The active device, including a gate, an oxide channel, a source and a drain, is connected to the scan line and the data line. The second insulating layer is disposed on the oxide channel and the linear transmitting part. The common electrode is disposed above the linear transmitting part. The first pixel electrode is connected to the drain.