Among those who received calls were two members from each the Army, Marine Corps, Navy, Air Force and Coast Guard.
In his weekly radio address, Mr. Obama also had a heartfelt message for our troops.
"We give thanks for all our men and women in uniform and for their families who are surely missing them very much today. We are grateful for their sacrifice too."
In Washington, President Barack Obama and his family paused to celebrate a quiet holiday at the White House Thursday.
The first family sat down and enjoyed turkey, honey-baked ham, cornbread stuffing, greens and all of the traditional fixings plus nearly 10 different pies for dessert.
Both the president and first lady also took to Twitter to tweet holiday thanks.
Obama tweeted, "Today, let's pledge to help our fellow Americans in need, because we are greater together than we are on our own. #HappyThanksgiving -bo."
While Michelle, tweeting from her FLOTUS account, thanked military families.
"This #Thanksgiving, let's give thanks for all our brave men & women in uniform and their families. We're so grateful for your sacrifice. -mo"
The "BO" and "MO" signature specifies the tweet was authored and sent directly from Barack Obama and Michelle Obama, respectively.
On Thanksgiving Eve, the first family continued a tradition and participated in a Thanksgiving service project by handing out food at the Capital Area Food Bank in Washington D.C.
It's the third straight Thanksgiving that the Obamas have helped out at this particular food bank, one of the largest serving the D.C. area. The Capital Area Food Bank distributes 30 million pounds of food annually.
Mr. Obama also continued a decades-old tradition when he officially pardoned the National Thanksgiving Turkey Wednesday. The pardon was issued to a gobbler named Popcorn and Caramel.
ABC News and The Associated Press contributed to this report.