The invention relates to a construction system for constructing a filling bag cofferdam by utilizing a small cutter-suction dredger. The construction system comprises a main small cutter-suction dredger. A material discharging end of the main small cutter-suction dredger is connected with a material conveying pipeline; the end part of the material conveying pipeline is connected with a main pipe orifice of a crossover tee; two bypasses are respectively connected with line distributing devices through material supplying pipes; and the line distributing devices are connected with filling bags through material supplying hoses. The construction method comprises the following steps of (1) preparing for construction; (2) positioning through positioning vessels when a tide level meets the requirement, and starting to lay the filling bags through positioning cables; (3) connecting the material conveying pipeline of the small cutter-suction dredger with connectors of the filling bags; (4) starting to construct through the small cutter-suction dredger, and filling filling materials into the filling bags; and (5) assigning a scheduling position on site, and according to the filling bag constructing condition, commanding to switch on and off material supplying pipe switches or change positions and continuously construct the next filling bag. The problems that an existing filling method is affected by natural conditions, so that the sand source transportation is difficult and the construction on the filling bags cannot be carried out, and the filling bags cannot be formed easily due to low construction efficiency caused by in-place soil fetching are solved.