Some studies have demonstrated that the assessments of autonomic activities from the alterations of heart rate variations (HRVs) after autonomic blockade and during exercise of high intensity by the spectral analysis of HRV seemed inconsistent with actual situation. The inconsistency is probably caused by the contributions of fluctuating magnitudes and mean levels of autonomic activities on HRV having not been clarified. The alterations of HRV after autonomic blockade and during exercise of high intensity using a mathematical model were simulated. The autonomic activity in normal condition was assumed first according to some experimental evidence. Then autonomic activities after sympathetic blockade, vagal blockade and during exercise of high intensity were appropriately adjusted accordingly. The HRVs in response to these given autonomic activities were simulated. We found that the effect on HRV influenced by the mean level of autonomic activity is helpful to explain alterations of HRV in these conditions. After vagal blockade, a largely reduced low frequency (LF) power could be caused by the reduced mean heartbeat interval induced by a decreased mean level of vagal activity. Increased low and high frequency powers after sympathetic blockade could be caused by the increased mean heartbeat interval induced by a decreased mean level of sympathetic activity. A decreased LF power during exercise of high intensity, in addition to the withdrawal of vagal activity, could also be caused by the decreased mean heartbeat interval induced by an increased mean level of sympathetic activity.