The Mexican midfielder picked up a knee ligament injury during training on Wednesday and will need to have surgery to correct the issue
The Mexico international, who came through the Barcelona academy and made three senior appearances this term, sustained the problem during a training session on Wednesday.
Subsequent tests revealed the full extent of the injury and the 23-year-old will undergo surgery on Nov. 5 to correct the issue.
A statement on the club's official website read: "Jonathan dos Santos will undergo arthroscopic surgery on November 5 to fix an injury in the anterior cruciate ligament of his right knee.
"He will be out for approximately six months, as reported by the club's medical department. It should be remembered that the Mexican midfielder was injured during training on Wednesday."
Dos Santos, who was promoted to the club's first team squad last term, has made a total of 28 appearances for the Blaugrana.
The surgery also puts his status for the World Cup into doubt, should El Tri qualify from a playoff against New Zealand. Dos Santos has six caps, but hasn't appeared for Mexico since 2012.