The invention provides a microfluidic detection system and a detection method thereof. The system comprises an MCU processor, a light source control IO, a 700nm characteristic variable frequency light source control circuit, a total phosphorus reagent disc chip, a PD receiving circuit, a small signal amplification and filter circuit and an AD sampling circuit. According to the microfluidic detection system and the detection method thereof, a characteristic frequency conversion signal is adopted for detection, so that the detection system and the detection method can be adaptive to different interference signals, including light source fluctuation, PD temperature drift fluctuation, zero drift and the like, the measurement precision is improved, and the error range is reduced.