To systematically evaluate coix germplasm across diverse environments and years, this study conducted a two-year field experiment (2023–2024) with 70 accessions at two contrasting altitude sites: Shimen (320 m, low altitude) and Luyang (750 m, high altitude). Seven key agronomic traits—plant height, stem diameter, tiller number, grains per plant, seed-setting rate, thousand-grain weight, and grain yield—were analyzed using variation, correlation, principal component, and cluster analyses. The results revealed rich phenotypic variation, with a significantly higher mean coefficient of variation at the low-altitude site (16.38%) than at the high-altitude site (12.63%), indicating greater phenotypic plasticity under lower altitude conditions. Most traits performed better at the high-altitude site, reflecting stronger ecological adaptability. Principal component analysis identified tiller number, seed-setting rate, thousand-grain weight, and grain yield as key traits influencing overall performance. Using a membership function-based comprehensive evaluation, 11 accessions with high adaptability across both altitudes were selected, among which YY17-33 (G70) performed most outstandingly, achieving an average annual grain yield of 307.14 kg/667 m2 and a seed-setting rate of 63.74% at Luyang. This study establishes a robust framework for multi-site, multi-year phenotypic evaluation of coix germplasm and provides elite genetic resources for breeding programs targeting different ecological regions.