In view of the current clinical practice, the detection of pathogenic bacteria mainly depends on bacterial culture methods. The methods have disadvantages of long cycle and low accuracy, and are prone to cross contamination and human infection. We propose the microfluidic chip based isothermal nucleic acid amplification for molecular diagnostics. An air-insulated microfluidic chip is designed for the automatic centrifugal distribution of samples to test cells. The confocal optical imaging, rotation scanning signal acquisition, thin layer air bath heating proportion-integral-derivative temperature control, etc. are developed. A microfluidic chip based nucleic acid analyzer is also developed. We detect the pathogens of respiratory tract using the proposed system, whose sensitivity can reach 10 copies. The sample reagent consumption is reduced to 0.94 μL, and the results can be obtained in 45 min. In a blinded experiment of 100 clinical patient sputum samples, the total coincidence rate of results of our system and the traditional polymerase chain reaction is over 98%. This novel nucleic acid analyzer is suitable for low cost and accurate medical applications in hospital, community care and township health clinic, etc.