I know there is no problem to reserve a hotel wit credit cards or debit cards on
Booking.com but I don't see anyone book a hotel with prepaid debit cards. Because I can just have prepaid debit card to do my online shopping, does this site accept prepaid card for booking?
The most important thing to note is this from https://www.booking.com/content/how_we_work.en-gb.html:
Booking.com doesn't charge the guest for any booking or cancellation fees nor any other fees related to their reservation, and no payment is made by Booking.com. The payment is directly charged by the provider.
As far as most sites go, however, there is no distinction between the two types of debit cards - it should take the payment the same as if it were a normal debit card. You'll just have to try it to see if the property owner you want to deal with accepts it.