Captain Jerry Kyd hailed a "truly seminal moment for Scotland" as he took command of the future flagship at Rosyth Dockyard in Fife.
The 65,000 tonne ship will be based at Portsmouth Naval Base
HMS Queen Elizabeth is one of the largest surface warships ever constructed for the UK.
A second carrier, HMS Prince of Wales, is still under construction in Rosyth.
Captain Kyd said the Queen Elizabeth will be tasked with "protecting British maritime power around the world wherever the government needs it".
He said maritime warfare has "changed very little" since the Battle of Jutland, 100 years ago next week, when Royal Navy battle cruisers set out to enforce a British blockade during the First  World War.
But the Queen Elizabeth will be equipped to deal with future threats, including unmanned aircraft, robotics and cyber attacks.
He added: "As a naval officer I always want more ships and more aircraft carriers, but I can't see in the foreseeable future two more ships of this scale being built in the United Kingdom".
The new commanding officer of HMS Queen Elizabeth has taken control of what he expects to be one of the last major aircraft carriers built in the UK.