The invention discloses an analysis device for integrated nucleic acid extraction and amplification detection based on a smart phone and a method thereof, which relates to the key technical field of intelligent medical instruments. According to the analysis device, the smart phone is used as a main component, the smart phone is integrated with microfluid driving, temperature control and multicolorfluorescence detection, a portable multifunctional universalization device integrating nucleic acid extraction, amplification and detection is formed, the device is combined with a micro-fluidic chip; on-chip nucleic acid extraction, isothermal amplification qualitative detection and detection of real-time fluorescent quantitative PCR (Quantitative Real-time PCR,qPCR) and multiple fluorescent PCR(Multiplex PCR) are realized, and analysis and detection of pathogen nucleic acid are realized. The analysis method comprises the steps of nucleic acid extraction, system configuration, system loading, temperature setting, image acquisition, image processing and result storage and sharing. The smart phone is used as a main component, the size is small, the cost is low, the functions are complete,the applicability is high, and the detection method is diversified.