This invention provides a transistor with an etching stop layer and a manufacturing method thereof. The transistor structure includes a substrate, a crystalline semiconductor layer, an etching stop structure, an ohmic contact layer, a source, a drain, a gate insulating layer, and a gate. The manufacturing method is performed by patterning the ohmic contact layer and the crystalline semiconductor layer at the same time with the same mask; and patterning the ohmic contact layer and the source/drain layer at the same time with another the same mask.