Background High-intensity interval training (HIIT) has been shown to enhance cardiovascular health. However, there is a lack of research investigating the specific cardiovascular effects of different HIIT training modes. Therefore, this study aimed to compare the acute effects of cycling-type high intensity interval training (C-HIIT) and resistance-type high intensity interval training (R-HIIT) on arterial stiffness, cardiac autonomic modulation, and cardiac biomarkers in healthy young men. Methods This is a cross-over randomized trial. Eleven healthy active young men took part in both C-HIIT and R-HIIT. Cardio-ankle vascular index (CAVI), heart rate variability (HRV), and systolic blood pressure (SBP) were measured before, immediately and 30 min after the exercise in C-HIIT and R-HIIT. Meanwhile, blood samples for cardiac troponin-T (cTnT) and amino-terminal pro-B-type natriuretic peptide (NT-proBNP) were assessed using ELISA before, 5min and 35min after exercise. Results There was a significant time x group interaction effect (P = 0.019, eta(2)(p) = 0.182) and time main effect for (sic)CAVI (P < 0.001, eta(2)(p) = 0.729), and R-HIIT resulted in a more significant reduction in (sic)CAVI compared to C-HIIT (- 0.60 +/- 0.30, P = 0.043, d = 0.924) immediately after exercise. There was a significant time main effect was observed for SBP (P = 0.001, eta(2)(p) = 0.304). A significant time main effect for lnHF (P < 0.001, eta(2)(p) = 0.782), lnRMSSD (P < 0.001, eta(2)(p) = 0.693), and LF/HF (P = 0.001, eta(2)(p) = 0.302) of HRV was observed. A significant time main effect was observed for cTnT (P = 0.023, eta(2)(p) = 0.193) and NT-proBNP (P = 0.001, eta(2)(p) = 0.334) of cardiac biomarkers. Conclusion R-HIIT and C-HIIT elicited similar acute responses in cardiac autonomic modulation and cardiac biomarkers. However, R-HIIT was more effective in reducing arterial stiffness in healthy young men. Furthermore, the increase in cardiac biomarkers induced by both C-HIIT and R-HIIT was reversible.