The think-tank Australian Strategic Policy Institute (ASPI) reported that around 16,000 mosques had been destroyed or damaged.
The Australian think-tank used satellite imagery for documenting hundreds of sacred sites and statistical modeling.
Rights groups have been vocal in expressing their concerns over human rights abuse in the region.
It is believed that over 1 million Uighurs and other mostly Muslim Turkic-speaking people have been incarcerated in camps across the northwestern territory.
Residents of the regions faced additional pressure to give up traditional and religious activities.
Most of the destruction had taken place in the last three years and an estimated 8,500 mosques had been completely destroyed, the report said, with more damage outside the urban centres of Urumqi and Kashgar.
Many mosques that escaped demolition had their domes and minarets removed, according to the research, which estimated fewer than 15,500 intact and damaged mosques left standing around Xinjiang.