The effects of gender and other contributory factors on pulse waveform are still under arguments. In view of different results caused by few considerations of possible influential factors and general agreement of gender relating to pulse waveform, this study aims to address the confounding factors interfering with the association between gender and pulse waveform characteristics. A novel method was proposed to noninvasively detect pressure pulse wave and assess the morphology of pulse wave. Forty healthy young subjects were included in the present research. Height, weight, systolic blood pressure (SBP), and diastolic blood pressure (DBP) were measured manually and body mass index (BMI), pulse blood pressure (PP) and heart rate (HR) were calculated automatically. Student's t test was used to analyze the gender difference and analysis of variance (ANOVA) to examine the effects of intrinsic factors. Univariate regression analysis was performed to assess the main factors on the waveform characteristics. Waveform features were found significantly different between genders. However this study indicates that the main factors for time-related and amplitude-related parameters are HR and SBP respectively. In conclusion, the impact of HR and SBP on pulse waveform features should not be underestimated, especially when analyzing the gender difference.