It is the main method for amplifying the specific gene to use the nucleic acid amplification system to accomplish polymerase chain reaction (PCR). The temperature retard between heat source and sample exists in the heating and cooling progresses of most nucleic acid amplification system. The retard would result in the problem that the sample would take a long time to reach the set temperature and the problem would reduce the speed of integrate reaction. Non-specific products would be created in the process of amplification when the sample cannot reach the set temperature within a certainly time and the amplified efficiency would be reduced. A miniaturization nucleic acid amplification system heated by air was designed in this study according to the principle of air-heated nucleic acid amplification system and the characteristics of the PCR instrument Smart-cycler. The heat transfer process was analyzed and the heat transfer time was calculated. The actual temperature was measured in real time, and the temperature curves were fitted. The heating time was chosen by analysis results and data fitting and the air temperature was changed, while the sample temperature was recorded. The retard between sample and air was optimized by choosing the best curve of sample temperature. The temperature retard between sample and air was reduced sharply and the required time of integrate progress is shortened to 50%. We confirmed from the amplification experiment of Listeria monocytogenes that the improved system could complete 3 cycles within 4 minutes, and the amplification effect was good. The amplification speed and effect could be improved effectively by optimizing the delay between sample and air.