How can I treat the blisters in between my toes?

A little more. Just a little more information is needed to separate the possible causes of your problem. Things like, how long? How many toes? Both feet? Is there itching? New shoes? I hope you can see what is need to exact a solution to your problem.
Toe Blisters. Moisture managment is paramount. Wash and dry feet thoroughly and use a drying agent or astringent to dry the skin. You can even sit in front of an oscillating fan to help dry them. Using a drying agent and antiseptic like betadine will certainly help, as well. Further, you may need to use an antiperspirant on your feet. You may also have a tinea (athletes foot) infection at the same time.
dry the area. Powder in between the toes to drive the area try an antifungal medication to prevent athletes foot.