Yes, the Wehrmacht refer to the German armed forces which included the Luftwaffe (air force) and the Kriegsmarine (Navy) and Heer (army), the Heer refers only to the German army. It would be the same difference between US armed forces and the US army.

In theory the Wehrmacht high command coordinated efforts between the three branches and had oversight over all three but in reality the Heer high command controlled units on the eastern front while the Wehrmacht command controlled units on the western and north African fronts. To complicate things further later on during the war the SS established its own combat branch (the Waffen-SS) which fielded more than two dozen ground divisions while maintaining an official command structure of both the Heer and the Wehrmacht.