Background: Cholangiocarcinoma, also referred to as bile duct cancer, is a major global health concern. The diagnosis of this cancer is often difficult due to its lack of distinctive symptoms and its tendency to present at advanced stages. However, the recent emergence of blood liquid biopsy as a diagnostic tool has shown great potential for detecting and managing cholangiocarcinoma. The use of blood liquid biopsy in East Asian populations, where the incidence of cholangiocarcinoma is particularly high, has the potential to improve the accuracy of diagnosis, prognosis, and targeted treatment planning. Methods: The study cohort contains 53 Chinese cholangiocarcinoma patients, the examination of DNA from tumor tissue (tDNA), blood (cfDNA), and blood leukocytes (gDNA) was performed using 680 gene targeted capture sequencing and analyzing for CNV, fusion, SNV, indel, MSI, and TMB. The sequencing depth was 2200X for tDNA, 20000X for bDNA, and 10000X for gDNA. In the tissue samples evidence of PD-L1 expression was examined. The TMB was classified as high (TMB-H) with a cutoff > 10 mutations/megabase and low (TMB-L) < 10. Microsatellite instability-high (MSI-H) was identified in cases where instability was observed > 20% of 117 loci, and the microsatellite stable (MSS) rate was determined to be < 20%. Results: In a cohort of 53 patients, a thorough analysis of tissue and blood samples was conducted to detect somatic mutations. 146 (38.1%) shared mutations were found in both tDNA and cfDNA, while 211 (55.09%) and 25 (6.53%) unique mutations were found in tDNA and cfDNA respectively. Of the 64 mutations found in CNV, 5 (7.81%) were shared in tDNA and cfDNA, 52 (81.25%) were unique in tissues, and 7 (10.93%) were unique in blood. High frequency mutated genes were also revealed as TP53, KRAS, SMAD4, LRP1B, and ARID1A, which were consistent with the results from the IntoGen database (4 cohorts, 393 samples). Notably, LRP1B (11.32%, 6/53) was not detected in the validation cohort. 96.23% of the samples showed consistent tTMB vs. bTMB outcomes, with only 1 sample exhibiting high PD-L1 expression and TMB-L, MSS, and 1 sample (out of 52 with MSS) having TMB-H and PD-L1 expression less than 1%. Conclusions: The results of the mutation analysis suggest that relying solely on cfDNA for molecular typing of cholangiocarcinoma is not sufficient. This highlights the importance of testing tissue samples in order to accurately detect tumor mutations in cholangiocarcinoma. Further research is needed to determine the significance of LRP1B, a gene that was frequently mutated in the study cohort but not found in the validation cohort, in the diagnosis and treatment of cholangiocarcinoma.