Cis-regulatory elements (CREs) direct precise gene expression for development and environmental response, yet their spatial organization in crops is largely unknown. We introduce transposase-accessible chromosome conformation capture (TAC-C), a method integrating ATAC-seq and Hi-C to capture fine-scale chromatin interactions in four major crops: rice, sorghum, maize, and wheat. TAC-C reveals a strong association between chromatin interaction frequency and gene expression, particularly emphasizing the conserved roles of chromatin interaction hub anchors and hub genes across crop species. Integrating chromatin structure with population genetics data highlights that chromatin loops connect distal regulatory elements to phenotypic variation. In addition, asymmetrical open chromatin interactions among subgenomes, driven by transposon insertions and sequence variations, contribute to biased homoeolog expression. Furthermore, TaSPL7/15 regulate photosynthesis-related genes through chromatin interactions, with enhanced photosynthetic efficiency and starch content in mutant. TAC-C provides insights into the spatial organization of regulatory elements in crops, especially for SPL-mediated photosynthesis regulation in wheat.