Actually I already found the answer in another forum, thanks to romeo.tran (http://www.leotheme.com/forum/20-general-pretashop-template-installation/3657-transparent-png-logo-in-prestashop.html):
1. login in back-office then access
Preferences > Images
2. in images tab, please config
Image quality : Use PNG only if the base image is in PNG format.
3. please access
Preferences > Themes
then upload png image for logo again