To investigate the prognostic significance of clinicopathological factors in patients with primary central nervous system lymphoma (PCNSL) in a single center. Patients newly diagnosed with PCNSL at our center were recruited between January 2019 and March 2023. Baseline demographic and clinicopathological data were collected retrospectively. The Kaplan–Meier method and Cox regression analysis were performed for survival analyses. A total of 118 patients were enrolled. The median age was 64 (IQR, 54–68). The median progression-free survival (PFS) and overall survival (OS) were 12.70 (95%CI, 9.73–23.30) months and 36.87 (95%CI, 25.57-NR) months, respectively. KPS < 70 and ECOG ≥ 3 were significantly associated with worse PFS and OS. High International Extranodal Lymphoma Study Group (IELSG) score (IELSG 4–5) and high-risk Memorial Sloan-Kettering Cancer Center (MSKCC) score were also adverse factors for PFS and OS. BTK inhibitors (BTKi) therapy (HR 0.39, 95% CI, 0.18–0.86, p = 0.020) and consolidation therapy (HR 0.19, 95% CI, 0.06–0.64, p = 0.007) were confirmed as independent favorable factors for OS. A high NK lymphocyte proportion was associated with worse OS (p = 0.008). Patients in the high NK lymphocyte group experienced a higher rate of primary tumor resistance (57.14%) than the low NK lymphocyte group (33.33%). KPS < 70, ECOG ≥ 3, IELSG 4–5, and high-risk MSKCC score are adverse factors for PFS and OS. Importantly, BTKi therapy and consolidation therapy are independent favorable factors for OS. Peripheral lymphocyte immunophenotyping could be a potential predictive indicator for prognosis and therapeutic response in PCNSL.