In advanced lung cancer patients, pleural effusion (PE) was proven to be a promising source of liquid biopsy. However, due to a lack of thorough evaluation of its potential compared with typical clinical samples, its clinical relevance was not commonly accepted. A total of 164 individuals with advanced lung cancer were included in the research, with 164 matched tumor tissue and PE-cfDNA, 153 accompanying plasma, and 63 1PE-sDNA. PE-cfDNA had a considerably higher median mutant allele frequency and a 65% overall mutation concordance rate with tissue than PE-sDNA (43%) and plasma-cfDNA (65%). Several genes, including SMARCA4, PIK3CA, ERBB2, KMT2A, ALK, and NF1, had significant differences between PE-cfDNA and tumor tissue. PE-cfDNA and tumor tissue have had an 87% concordance rate for clinically actionable mutations. Furthermore, 11 patients were found to have actionable mutations in PE-cfDNA, and 4 of them benefited from targeted PE-cfDNA therapy. Meanwhile, when tumor tissue or tumor tissue from other origins was unavailable, PE-cfDNA recapitulated mutations from various tissue origins and offered more mutational information. Compared with tumor tissue alone, the combination of tumor tissue and PE-cfDNA profiling enhanced positive patient detection rates. The outcomes underscored the importance of PE-cfDNA in the proper selection of patients for targeted therapy. PE-cfDNA-based liquid biopsy outperforms PE-sDNA and plasma-cfDNA in identifying gene changes. PE-cfDNA in combination with tumor tissue profiling allowed for a more extensive genetic profile of lung cancer patients, which could have been helpful for improved patient selection and treatment management.