Lipid droplet (LD) is a main storage site of neutral lipids in cells. It widely exists through all organisms. Recent studies demonstrate that LD is not only an energy container, but also a multifunctional organelle that is complicated and dynamic. Aberrant lipid storage leads to many metabolic diseases, including atherosclerosis and diabetes mellitus. Caenorhabditis elegans (C. elegans) is a good model organism for genetic modification. Our previous study identified a C. elegans LD marker protein, DHS-3 that is almost exclusively localized on C. elegans LDs, indicating that it can be used for RNA interference screening to determine neutral lipid storage regulators of C. elegans. Here we report our whole-genome RNA interference screening of C. elegans with DHS-3::GFP as LD marker. From 16749 genes, finally, we identified 78 genes that caused significant LD phenotypes. Among them, 30 genes increased LD size, 9 genes reduced LD size, 22 genes decreased LDs, and 24 genes induced LD aggregation. These results will facilitate LD study using this powerful genetic model system, C. elegans, and furthermore impact the study of lipid metabolic diseases.