The invention discloses a silicon transistor with a double super-shallow isolation structure and a manufacturing method thereof. The manufacturing method comprises the following steps: firstly, providing a silicon substrate, forming a first super-shallow channel structure and a second super-shallow channel structure in the substrate, forming a first type doped region serving as a collector electrode, and forming a second type light doped region serving as a base electrode in a silicon layer between the two super-shallow channel structures; secondly, forming a second type doped region in the silicon substrate to make the first and second doped regions adjacent to the first and second super-shallow channel structures and the second type light doped region; and finally, forming a first type emitting electrode structure on the surface of the second type light doped region. The internal resistance of a base electrode connecting wire connected with the base electrode is decreased so as to improve the current driving force of a whole device.