Type of data:Raw and processed multispectral images (.raw, .hdr, .bpm, .txt), tabular phenotypic and feature data (.xlsx), machine learning scripts (.pdf).Data collection:Field-measured data of soybeans under 4 experimental treatments across 2 growing seasons, as well as corresponding multispectral data, were collected. UAV images were captured using a Specvision multispectral camera mounted on a DJI M300 RTK UAV. Data acquisition was conducted between February and August 2025, from 10:00 AM to 2:00 PM local time, under sunny and windless weather conditions, in Datian Town, Dongfang, Hainan. Five key growth stages were targeted, namely the seedling stage, branching stage, initial pod stage, full pod stage, and seed-filling stage. During image acquisition, a gray cloth was placed on-site and used for radiometric calibration during the image processing phase.