Rice blast, caused by Magnaporthe oryzae, is a devastating disease that jeopardizes global rice production and food security. Precision agriculture demands timely and accurate monitoring tools to enable targeted intervention. This study introduces a novel deep learning framework that fuses time-series hyperspectral imaging with an advanced Autoformer model (AutoMSD) to dynamically track rice blast progression. The proposed AutoMSD model integrates multi-scale convolution and adaptive sequence decomposition, effectively decoding complex spatio-temporal patterns associated with disease development. When deployed on a 7-day hyperspectral dataset, AutoMSD achieved 86.67% prediction accuracy using only 3 days of historical data, surpassing conventional approaches. This accuracy at an early infection stage underscores the model’s strong potential for practical field deployment. Our work provides a scalable and robust decision-support tool that paves the way for site-specific disease management, reduced pesticide usage, and enhanced sustainability in rice cultivation systems.