The invention relates to a micro-fluidic chip focusing control system and a micro-fluidic chip fluorescence detection system. The micro-fluidic chip focusing control system comprises a light emitting device, a scattered light detection device, a moving device and a control device, wherein the light emitting device emits exciting light to a micro-fluidic chip; the scattered light detection device collects the light intensity of the scattered light of the micro-fluidic chip to obtain an intensity value and sends the intensity value to the control device; the control device controls the moving device to drive the micro-fluidic chip to move in the preset direction in the fixed plane, so that the exciting light sequentially approaches to, irradiates and leaves far away from the flow passage of the micro-fluidic chip, obtains the displacement of the micro-fluidic chip and receives the intensity values of different displacement positions collected by the scattered light detection device; the control device generates an intensity curve corresponding to the fixed plane according to the intensity values, obtains the focusing position points of the micro-fluidic chip according to the intensity curve, and controls the moving device to drive the micro-fluidic chip to move to the focusing position point. Therefore the focusing can be automatically performed; the accuracy is high; the cost is low.