In the modern era, mobile device and cloud database have become ubiquitous which provides unprecedented opportunity for psychologists and neuroscientists to develop personalized music therapy for mental stress relief. However few of studies go further to compare the effect of different music genres and the timing of listening to music on stress relief, and none uniquely integrates heart rate variability (HRV)-based physiological evidence together. Therefore, this study aims to analyze the impact of different music types (classic vs self-selected relaxing music) as well as timing of listening to music (before vs during vs after stress stimulus tasks) on HRV evidence-based stress recovery. Forty-eight healthy young males were randomly assigned to either preferred relaxing music or classic music group or control group (rest in silence). HRV parameters in time and frequency domain as well as self-reported stress scores were assessed. Results show that the averaged stress score in classic group is slightly lower (no statistical difference) than that in personal preferred music group, while both HRV time and frequency parameters were significantly different between the two genres. These results not only reveal that classic music is more effective than personalized relaxing music, but also indicate that physiological parameters are able to provide much more richer emotional information if compared to pure subjective assessment. Regarding the timing of listening to music, there is no mutually statistical difference, indicating that listening to music before, during and after the stressful events has a similar relief effect.