The invention discloses a light source compensation method and device for confocal type LED induced fluorescence detection. The method comprises the following steps: acquiring a microfluidics biochipscanning signal and an LED light source fluctuation signal; establishing a coordinate system, fitting the LED light source fluctuation signal by using negative exponential distribution so as to acquire an LED light source change tendency signal; extracting a detection area scanning signal and a quality inspection area scanning signal in the microfluidics biochip scanning signal, a detection area LED light source change tendency signal in the detection area scanning signal time quantum, and the quality inspection area LED light source change tendency signal in the quality inspection area scanning signal time quantum; computing an initial detection result of a microfluidics biochip, acquiring a light source compensation factor to correct the initial detection result of the microfluidics biochip, thereby obtaining a final detection result of the microfluidics biochip. The method disclosed by the invention can effectively improve the accuracy, the stability, the consistency and the repeatability of the detection.