The 25-year-old former Swansea player requires surgery to fix the problem, with his time on the sidelines likely to be around the six-week mark.
"Jon will undergo an operation on Friday and faces a possible six week lay-off," said Ospreys physio Chris Towers.
"Jonathan has been suffering from an ongoing groin injury that, although up until now hasn't stopped him playing, has gradually worsened.
"Having assessed his condition on Wednesday, a decision was made to refer him to a specialist today, who has identified the need for surgery."
Thomas was in superb form last year as he helped his country claim Grand Slam glory and his club win the EDF Energy Cup.
His abilities in the line out will make it hard for Wales coach Warren Gatland to find a like-for-like replacement, although 2005 Lion Michael Owen could be one player to benefit from Thomas' misfortune.
Owen captained Wales to the Grand Slam three years ago before leading the Lions against Argentina at the Millennium Stadium, but he has since fallen out of favour and will be keen to reclaim a place in the Welsh squad.