This integrated ubiquitylome–proteome dataset provides a comprehensive view of protein abundance and lysine ubiquitination dynamics in the commercially important red alga Gracilariopsis lemaneiformis under low-temperature stress. The ubiquitylome was profiled using anti-K-ε-GG antibody-based enrichment followed by high-resolution liquid chromatography–tandem mass spectrometry (LC-MS/MS), while the global proteome was quantified in parallel under the same experimental conditions. The dataset includes identification and quantification of thousands of proteins and ubiquitination sites, enabling systematic analysis of post-translational regulatory networks involved in cold stress response. This resource offers valuable insights into the molecular mechanisms of environmental adaptation in marine macroalgae and serves as a foundation for future functional studies on ubiquitin-mediated signaling in photosynthetic eukaryotes.