Objective This study was to compare the effects of the same workload of cycling intervention on hemodynamics between athletes and sedentary controls in order to find an effective exercise mode to prevent and reverse arterial stiffness. Methods Ten female college basketball athletes (BA) and ten age-matched controls (AC) were recruited and successively underwent four stages of cycling intervention. At baseline and after intervention, ultrasonic Doppler techniques were used to measure and calculate hemodynamic variables in carotid arteries including heart rate(HR), blood pressure(BP), arterial stiffness, arterial diameters(AD), center-line velocity(CV), pulsatility index(PI), blood flow rates(FR), circumferential strain(CS) and wall shear stress(WSS). Results Compared with AC at baseline, BA demonstrated: lower arterial stiffness, larger AD, lower HR and CV, higher mean FR, lower systolic and mean BP, lower max and mean WSS, higher min WSS. After intervention, both groups showed: CS, HR, CV, max and min FR, systolic BP, max and mean WSS increased significantly. Compared with AC after the same workload of cycling intervention, BA demonstrated: lower Arterial stiffness and larger AD, lower HR, CV, PI, systolic BP, max and mean WSS, and higher diastolic BP. Conclusions The arteries in BA demonstrated a better compliance in response to the same workload of acute intervention. The improved arterial structure and function in BA (decreased arterial stiffness and larger AD) might result from long-term basketball training and lead a better resting blood supply to brain. In addition, AC showed higher oscillatory WSS and increased arterial stiffness compared with BA. Long-term acute cycling exercise might have a detrimental effect on common carotid arterial structure and function.