Abstract Background The incidence rate of esophageal cancer in Asia is mainly squamous cell carcinoma, which is characterized by high mortality and poor prognosis. The prognosis of tumors is not only related to the biological characteristics of tumor cells, but also closely related to the nutritional status and inflammatory response of patients. The aim of this study is to investigate the relationship between nutritional index (PNI) and inflammatory response markers (NLR, LMR) at 90 days after surgery and long-term survival in patients with esophageal squamous cell carcinoma. To provide reference for accurately assessing the condition, identifying survival risks, and improving long-term prognosis. Methods The data of ESCC patients who underwent radical resection for esophageal cancer from April 2018 to November 2018 were extracted (n = 66). Calculate the prognostic nutritional index (PNI), neutrophil-to-lymphocyte ratio (NLR), lymphocyte-to-monocyte ratio (LMR) and other indicators of patients at 90 days after operation. ROC was used to calculate the cut-off values of PNI, NLR, and LMR. KaplanMeier survival curve was used to analyze the relationship between different PNI, NLR, LMR levels and long-term survival of patients. All patients were followed up regularly after surgery, and the last follow-up time was April 2023. Results The best cut-off values of PNI, NLR, and LMR were 42.8, 3.27, and 4.76, respectively. Kaplan Meier survival analysis showed a correlation between postoperative PNI, NLR, LMR at 90 days and overall survival and disease-free survival. At 90 days after surgery, the OS (P = 0.007) and DFS (P = 0.038) of patients in the high PNI group (PNI ≥ 42.8) were better than those in the low PNI group; The OS (P = 0.002) and DFS (P = 0.048) of patients in the low NLR group (NLR < 3.27) were better than those in the high NLR group; The OS (P = 0.001) and DFS (P = 0.039) of patients in the high LMR group (LMR ≥ 4.76) were better than those in the low LMR group. Conclusions PNI, NLR, and LMR are important predictors of OS and DFS in patients with esophageal squamous cell carcinoma after radical resection of esophagus. Patients with PNI ≥ 42.8, NLR<3.27, and LMR ≥ 4.76 at 90 days after surgery have better OS and DFS.