Abstract: AIM To analyze the changes of heart rate variability (HRV) in a naval population of a large navy surface ship. METHODS The study analyzed the heart rate variability from Holter recording in 263 naval personnel while at sea and 50 of them also had Holter monitoring. The results were compared and the correlation of aboard work time and heart rate variability was analyzed. RESULTSRMS SD, PNN50 and HF during tasks were lower than those before the task (P<0.05). Some parameters of HRV in crews from the Aviation Department, Mechanical and Electrical Department, Ships Department and Weapons and Security Department were lower than those in crews of Medical and Department and Administrative Department (P<0.05, P<0.01). The triangular index in Ships Department was lower than that in Weapons and Security Department. RMSSD, PNN50, HF and Triangular index in Mechanical and Electrical Department were lower than those in the Weapons and Security Department (P<0.05). The naval crews’aboard work time was negatively correlated with SDNN, SDANN, RMSSD, PNN50, HF and LF (P<0.05). CONCLUSION Working environment on surface ships reduces the crews’heart rate variability and effects automatic nerve function, but the degree of this changes is different when compared between different departments.