The official Communist Party watchdog also promised to prosecute Zhao Xinwei for "serious discipline breaches", which generally refers to corruption.
His paper covered the restive western region that has seen deadly clashes between police and ethnic Uighurs.
Mr Zhao is alleged to have "improperly discussed" party policies in the region, including combating terrorism.
The former editor is accused of failing to follow the party line on separatism, religion, extremism and other sensitive issues
His "words and deeds were not in line with the centre or regional party committee", a statement on the watchdog's website said.
It went on to say that he had "publicly made comments in opposition".
Mr Zhao has been expelled from the party and his case has been passed to the legal authorities, the watchdog said.
In recent months, China has brought in new rules tightening restrictions on criticism of party policy.
Uighurs and Xinjiang
Who are the Uighurs?
The editor of Chinese state newspaper Xinjiang Daily has been criticised for not following official policy.