Peripheral blood measurement based on tissue biopsy confirmation may facilitate the discovery of new diagnostic and therapeutic biological markers for pulmonary sarcoidosis. The gene expression levels of mediastinal lymph nodes were estimated by RNA immunoprecipitation sequencing. Biopsy samples from three pulmonary sarcoidosis patients were retrieved by mediastinoscopy or thoracoscopy surgery in Shanghai Pulmonary Hospital and three biopsy samples from patients with in situ lung carcinoma were utilized as normal controls. The public transcriptomic dataset GSE34608 was leveraged, in which whole blood gene expression from 18 pulmonary sarcoidosis patients and 18 healthy controls was available. The genes changing in the same direction in two kinds of samples were recognized as common differentially expressed genes (DEGs). Bioinformatics analysis was applied to identify the hub DEGs and to explore the potential mechanism. Ultimately, the validation of hub DEGs’ expression levels was conducted in PBMC samples from 9 patients diagnosed with pulmonary sarcoidosis and a control group consisting of 7 healthy individuals. A total of 138 common DEGs were screened from mediastinal lymph nodes and peripheral whole blood. Among them, 6 hub DEGs including CTSS, CYBB, FPR2, MNDA, TLR1 and TLR8 were identified by PPI network and further verified by qRT-PCR using PBMC samples. The most significant functional pathways were immune response, inflammatory response, plasma membrane and extracellular exosome, with 6 hub genes distributing along these pathways. In conclusion, CTSS, CYBB, FPR2, MNDA, TLR1, and TLR8 could be conducive to improving the diagnostic process and understanding the underlying mechanisms of pulmonary sarcoidosis.