A semiconductor device and a manufacturing method of a semiconductor device thereof are provided. The manufacturing method includes the following steps. Two stacked structures are formed a substrate. Each of the stacked structures includes a plurality of gate layers, a plurality of gate insulating layers and a top insulating layer. A charge trapping structure and a channel layer are formed. The charge trapping structure includes a plurality of first dielectric layers and a plurality of second dielectric layers. Part of each of first dielectric layers is etched and part of each of second dielectric layers is etched to expose part of the channel layer. A landing pad layer is formed on the first dielectric layers and the second dielectric layers to connect the channel layer.