The invention relates to a detection method of a microfluidic chip based on a photoacoustic technique and a device thereof. The detection method comprises the following steps of: adopting the microfluidic chip consisting of an incident light generating unit A, a photoacoustic signal detection unit B, a signal processing and data conversion unit C, a computer processing unit D and a platform capable of translating in double directions of X direction and Y direction; adding pretreated samples to be detected into the microfluidic chip for electrophoresis, emitting signals by the computer processing unit according to commands, and controlling electrophoresis and high voltage after being converted by a single chip microprocessor D/A; under the effect of electric field, separating samples with different mobility according to different mobility, absorbing light power by the samples to generate photoacoustic signals by a spot detection window, collecting photoacoustic signals by an ultrasonicsensor, converting the photoacoustic signals into electric signals, converting the photoacoustic signals received by the sensor into digital signals by an analog-to-digital converter and being capable of determining the types and properties of the samples to be detected after being processed by signals of the computer. The detection method has the advantages of high sensitivity, low cost and convenient operation.