I plan to travel from Beijing to Kashgar hopefully in the first week of July.

From Beijing, there is no direct train to Kashi, you can take a train to Urumqi first, then transfer to another train to Kashi, but the travel time is quite long, about several days.
There is also no direct flight, and you also need to transit in Urumqi, and the fare is much higher than train, but the travel time is shorter.

Near the railway station, I’m afraid you cannot find such a Muslim Hotel. But several other hotels are available nearby:
Keshi Express Hotel, located near the Exit of the train station.
Jinyouyuan Hostel, located at about 25 yards to the south of the station exit. And near the airport, there is an Airport Hotel, located at No. 473 of Jichang Road.

Although you cannot find muslim hotels, you can easily find many muslim restaurants, most restaurants offer the halal food. Have a try.

Thank you Nancy! I've another plan. I want to divide my journey as following:
1) I want to stop midway b/w Beijing to Urumqi.
2) I want to stop midway b/w Urumqi to Kashgar.
But I don't know about the midway city. Can you kindly let me know about it so that I can plan to stay overnight at the midway stops and enjoy the beauty of those cities?

Thanks a lot!

Well, from Beijing to Urumqi, you can stop at Jiayuguan.
In this city, Jiayuguan Pass, Overhanging Great Wall, The First Fire Tower of the Great Wall and Wei-Jin Art Gallery are popular scenic spots.

From Urumqi to Kashgar, Aksu is an ideal transit city. It also contains popular scenic spots, such as Kuqa Mosque, Thousand Buddhas Cave of Kizil and Subashi Ruins.

Have a good trip!

Waoooo, that's so helpful and valuable! Thank you so much for playing such an important role in planning of my tour! Stay Blessed!

Best Wishes for Whole Team of Travel China Guide!