Leaf color mutations provide valuable genetic resources for elucidating the molecular regulatory mechanisms of plant growth, and serve as efficient tools for screening offspring in crossbreeding. In this study, a Tartary buckwheat (Fagopyrum tataricum) mutant with yellow‐green leaves (yl1) was isolated from 60Co‐γ‐radiation mutation bank. Compared to WT, yl1 showed similar biomass and yield, despite a lower chlorophyll content and net photosynthetic rate. However, yl1 displayed significantly higher total phosphorus content after 14 d of medium and low phosphorus treatment. By using yl1 as the maternal parent, hybrid offspring could be visually distinguished at the cotyledon stage. Genetic analysis revealed that the yl1 phenotype was attributed to a single recessive mutation. Combined metabolome and transcriptome analysis identified 205 DEMs and 123 DEGs enriched in 30 pathways or metabolisms between yl1 and WT. Remarkably, the up‐regulation of SPX3, 5PTase2, PHO1, PAP3, PAP2, PAP7, and IPAP16, which are involved in enhancing phosphorus absorption, assimilation, transport, and remobilization, along with PLDζ1, GDPD1, MGD2, and NPC4L, which contribute to improving lipid metabolism, collectively resulted in high accumulation of 41 phosphorus‐containing DEMs (including 37 lipids) in yl1. This study emphasizes the potential of yl1 for effective screening of offspring and uncovers the interplay between photosynthesis and lipid metabolism, providing valuable insights to improve phosphorus use efficiency in Tartary buckwheat.This article is protected by copyright. All rights reserved