The invention discloses a smart control system for a subsea tree and a control method thereof. The smart control system comprises a water-surface master control station, an umbilical cable, a subsea control module and the subsea tree, wherein the master control station comprises a water-surface control station and a water-surface PLC control system. Data of the subsea tree is monitored through a sensor installed on the subsea tree, the water-surface PLC control system extracts and analyzes monitored data, monitors data on a real-time basis and sends corresponding control instructions to the subsea control module through the umbilical cable to further control the subsea control module to complete control functions. The control method of the water-surface PLC control system involves five aspects including production system, data processing, dynamic instrument monitoring, flow control and signal transmission, wherein the production system includes a normal production flow, a maintenance flow, a working flow and an emergency flow. A water-surface PLC control system is additionally installed to realize automatic control of the subsea tree, and the control precision and reaction speed are greatly improved.