During the rice quality testing process, the precise segmentation and extraction of grain pixels is a key technique for accurately determining the quality of each seed. Due to the similar physical characteristics, small particles and dense distributions of rice seeds, properly analysing rice is a difficult problem in the field of target segmentation. In this paper, a network called SY-net, which consists of a feature extractor module, a feature pyramid fusion module, a prediction head module and a prototype mask generation module, is proposed for rice seed instance segmentation. In the feature extraction module, a transformer backbone is used to improve the ability of the network to learn rice seed features; in the pyramid fusion module and the prediction head module, a six-layer feature fusion network and a parallel prediction head structure are employed to enhance the utilization of feature information; and in the prototype mask generation module, a large feature map is used to generate high-quality masks. Training and testing were performed on two public datasets and one private rice seed dataset. The results showed that SY-net achieved a mean average precision (mAP) of 90.71% for the private rice seed dataset and an average precision (AP) of 16.5% with small targets in COCO2017. The network improved the efficiency of rice seed segmentation and showed excellent application prospects in performing rice seed quality testing.