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Plant height is a vital agronomic trait that greatly determines crop yields because of the close relationship between plant height and lodging resistance. Legumes play a unique role in the worldwide agriculture; however, little attention has been given to the molecular basis of their height. Here, we characterized the first dwarf mutant <i>mini plant 1</i> (<i>mnp1</i>) of the model legume plant <i>Medicago truncatula</i>. Our study found that both cell length and the cell number of internodes were reduced in a <i>mnp1</i> mutant. Using the forward genetic screening and subsequent whole-genome resequencing approach, we cloned the <i>MNP1</i> gene and found that it encodes a putative copalyl diphosphate synthase (CPS) implicated in the first step of gibberellin (GA) biosynthesis. MNP1 was highly homologous to <i>Pisum sativum</i> LS. The subcellular localization showed that MNP1 was located in the chloroplast. Further analysis indicated that GA₃ could significantly restore the plant height of <i>mnp1-1</i>, and expression of <i>MNP1</i> in a <i>cps1</i> mutant of <i>Arabidopsis</i> partially rescued its mini-plant phenotype, indicating the conservation function of MNP1 in GA biosynthesis. Our results provide valuable information for understanding the genetic regulation of plant height in <i>M. truncatula.</i>