With their advantages in specificity, high stability and easy screening, aptamers are becoming increasingly popular recognition elements for biosensor platforms. At the same time, microchips as the new analytical detection platforms have achieved significant growth in the past decades. At present, with the intersection of aptamer and microfluidic technology, aptamer-based high-sensitivity bioanalysis on microchips exhibits a great application potential in biomedical science and environmental fields. In this review, we highlight the recent progress in high-sensitivity bioanalytical applications based on aptamer signal amplification strategies on microchips. Furthermore, the main challenges in the practical application are discussed, and the development in the future is prospected.