Understanding the dietary preferences of ancient societies and their evolution across periods and regions is crucial for revealing human-environment interactions. Seeds, as important archaeological artifacts, represent a fundamental subject of archaeobotanical research. However, traditional studies rely heavily on expert knowledge, which is often time-consuming and inefficient. Intelligent analysis methods have made progress in various fields of archaeology, but there remains a research gap in data and methods in archaeobotany, especially in the classification task of ancient plant seeds. To address this, we construct the first Ancient Plant Seed Image Classification (APS) dataset. It contains 8,340 images from 17 genus- or species-level seed categories excavated from 18 archaeological sites across China. In addition, we design a framework specifically for the ancient plant seed classification task (APSNet), which introduces the scale feature (size) of seeds based on learning fine-grained information to guide the network in discovering key "evidence" for sufficient classification. Specifically, we design a Size Perception and Embedding (SPE) module in the encoder part to explicitly extract size information for the purpose of complementing fine-grained information. We propose an Asynchronous Decoupled Decoding (ADD) architecture based on traditional progressive learning to decode features from both channel and spatial perspectives, enabling efficient learning of discriminative features. In both quantitative and qualitative analyses, our approach surpasses existing state-of-the-art image classification methods, achieving an accuracy of 90.5%. This demonstrates that our work provides an effective tool for large-scale, systematic archaeological research.