This dataset presents the results of a label-free quantitative proteomic analysis of seed mucilage (from 10 DPA siliques) of Arabidopsis thaliana wild-type (WT) and upl3 mutant plants. UPL3 encodes a HECT-type E3 ubiquitin ligase; by identifying differentially expressed proteins between WT and upl3, we focused on proteins related to cell wall polysaccharides, aiming to investigate the molecular mechanism by which UPL3 regulates seed mucilage structure. The dataset includes raw mass spectrometry data, protein identification results, and quantitative information of differential proteins, which can provide data support for research on the regulation of plant cell wall biosynthesis.