Exact yield estimation of fruits on plants guaranteed fine and timely decisions on harvesting and marketing practices. Automatic yield estimation based on unmanned agriculture offers a viable solution for large orchards. Recent years have witnessed notable progress in computer vision with deep learning for yield estimation. Yet, the current practice of vision-based yield estimation with successive frames may engender fairly great error because of the double counting of repeat fruits in different images. The goal of this study is to provide a wise framework for fruit yield estimation in sequence images. Specifically, the anchor-free detection architecture (CenterNet) is utilized to detect fruits in sequence images from videos collected in the apple orchard and orange orchard. In order to avoid double counts of a single fruit between different images in an image sequence, the patch matching model is designed with the Kuhn–Munkres algorithm to optimize the paring process of repeat fruits in a one-to-one assignment manner for the sound performance of fruit yield estimation. Experimental results show that the CenterNet model can successfully detect fruits, including apples and oranges, in sequence images and achieved a mean Average Precision (mAP) of 0.939 under an IoU of 0.5. The designed patch matching model obtained an F1-Score of 0.816 and 0.864 for both apples and oranges with good accuracy, precision, and recall, which outperforms the performance of the reference method. The proposed pipeline for the fruit yield estimation in the test image sequences agreed well with the ground truth, resulting in a squared correlation coefficient of R²_apple = 0.9737 and R²_orange = 0.9562, with a low Root Mean Square Error (RMSE) for these two varieties of fruit.