Plant biomass is an important agronomic trait that has been subjected to intense human selection for yield improvement. The underlying mechanism regulating biomass formation is currently gaining increasing attention, but it remains unexplored. In this study, we isolated a cucumber (Cucumis sativus L.) minicuke mutant with remarkably reduced biomass. The causative gene was identified as CsNMT1, a homologue of the Arabidopsis thaliana N-myristoyltransferase1. Our clustered regularly interspaced shot palindromic repeat-based genome editing confirmed the key role of CsNMT1 in biomass regulation. Multi-omics analyses integrating metabolomic and transcriptomic analyses revealed the suppression of a very early step of lignin biosynthesis and the corresponding down-regulation of genes involved in lignin biosynthesis in the minicikue mutant, suggesting an unexpected pathway for regulating biomass accumulation through lignin sink strength. Our findings demonstrate the function of NMT1 in regulating plant biomass and its potential application value for biomass improvement in cucurbits.