Accumulating evidence has indicated that long non-coding RNAs (lncRNAs) play critical roles in the development and progression of cancers, including esophageal squamous cell carcinoma (ESCC). However, the mechanisms of lncRNAs in ESCC are still incompletely understood and therapeutic attempts forin vivotargeting cancer-associated lncRNA remain a challenge. By RNA-sequencing analysis, we identified thatLLNLR-299G3.1was a novel ESCC-associated lncRNA.LLNLR-299G3.1was up-regulated in ESCC tissues and cells and promoted ESCC cell proliferation and invasion. Silencing ofLLNLR-299G3.1with ASO (antisense oligonucleotide) resulted in opposite effects. Mechanistically,LLNLR-299G3.1bound to cancer-associated RNA binding proteins and regulated the expression of cancer-related genes, including OSM, TNFRSF4, HRH3, and SSTR3. ChIRP-seq (chromatin isolation by RNA purification and sequencing) revealed that these genes contained enriched chromatin binding sites forLLNLR-299G3.1. Rescue experiments confirmed that the effects ofLLNLR-299G3.1on ESCC cell proliferation were dependent on interaction with HRH3 and TNFRSF4. Therapeutically, intravenous delivery of placental chondroitin sulfate A binding peptide-coated nanoparticles containing antisense oligonucleotide (pICSA-BP-ANPs) strongly inhibited ESCC tumor growth and significantly improved animal survivalin vivo. Overall, our results suggest thatLLNLR-299G3.1promotes ESCC malignancy through regulating gene-chromatin interactions and targeting ESCC by pICSA-BP-ANPs may be an effective strategy for the treatment of lncRNA-associated ESCC.