Moustache hostel is the best option for backpackers to stay. There are many transportation modes available to reach Jaisalmer, depending on your origin point. If you are starting from Delhi (the capital of India), then you can reach using a flight, bus, or even a train. You should even try to reach Jaipur or Jodhpur first if you are traveling from far away.
Source: https://www.moustachescapes.com/accommodation/Hostel/jaisalmer