Background <p>The objective of this study was to evaluate the significance of preoperative heart rate variability (HRV) as a surrogate marker for vagus nerve activity in predicting the incidence of postoperative pneumonia (POP) and lung function recovery in patients undergoing lung cancer surgery.</p> Method <p>A prospective observational study was conducted at a single center. Patients were categorized into two groups: the POP group, which included those who developed pneumonia post-surgery, and the non-POP group, comprising patients who did not experience POP.</p> Results <p>A total of 257 subjects met the inclusion criteria and were ultimately included in the study. 33 patients presented POP, accounting for 12.8% (33/257) of the patients. Logistic regression revealed that preRMSSD (OR: 0.812, 95%CI: 0.720–0.912, <i>P</i> = 0.001) and preHFP (OR: 0.990, 95%CI: 0.983–0.996, <i>P</i> = 0.002) were the independent factors for POP; receiver operating characteristic curve (ROC) analysis for predicting the occurrence of the POP revealed that the combination of BMI, preHFP and preRMSSD showed the positive diagnostic accuracy (AUC: 0.867, <i>P</i> &lt; 0.001). A logistic regression analysis showed that HRV indicators including preRMSSD (OR: 0.937, 95%CI: 0.892–0.985, <i>P</i> = 0.010) and preHFP (OR: 0.995, 95%CI: 0.992–0.998, <i>P</i> = 0.001) were independent factors for well-recovery in FEV1% within postoperative 30 days. Similar results can be found in well-recovery in FVC% or DLCO%.</p> Conclusion <p>These findings provided compelling evidence supporting the utility of HRV indicators in predicting both POP and postoperative lung function recovery among surgical lung cancer patients.</p> Trial registration <p>ChiCTR2400085997, registered in 24/06/2024.</p>