A new acoustic analysis system based on MEMS microphones has been developed for assessing the internal quality of fruits. Although acoustic analysis is one of the effective techniques for assessing the internal qualities such as firmness, maturity, hollowness and sweetness of fruits, it has not been widely applied for fruits quality assessment in practice because the conventional apparatus was complexed and bulky to suppress the effects of surrounding noise and to maintain a good frequency response of the system. This study aimed to achieve both noise suppression and good frequency response with a simple system structure using an ultra-low-cost MEMS microphone. By placing the MEMS microphone inside a specially-designed fruit holder and optimizing its arrangement with a tapping module, the effect of ambient noise was significantly suppressed compared with the MEMS microphone alone, realizing a drastic simplification of the system. The simple correlation analysis of watermelon sweetness and the received acoustic frequency revealed a high correlation coefficient of –0.82. This result not only demonstrates a high potential of the proposed system in non-destructive internal quality assessment of fruits, and also strongly suggests the possibility of further study on acoustic analysis based on machine-learning with large-scale data collected effectively by using the developed system.