Sharp finishing in the second half from the O's punished some terrible defending and glaring mistakes from home keeper Ben Williams.
Martin Ling's side dominated for long periods but had not looked like scoring when Justin Miller's snapshot was spilled by Williams allowing Adam Chambers an easy close-range finish a minute before half time.
And when Gary Alexander hit a perfectly weighted cross over the six yard box for Wayne Corden to deposit home at the far post with a first time finish the game was almost over.
Crewe had been absolutely dreadful despite some decent recent form and the closest they had gone in the first 45 was when Ryan Lowe curled a free kick just wide in stoppage time.
Dario Gradi threw on Michael Higdon and Lee Matthews in place of Rodney Jack and David Vaughan but it made little difference for The Railwaymen and there was more comical defending to come as the Londoners were gifted their third goal in the 67th minute.
Julien Baudet and Williams hesitated dealing with a high ball and Jabo Ibehre was left with the opportunity to walk the ball in after the two Crewe men had collided with each other.
Matthew Lockwood flicked the crossbar with a delightful 20-yard lob as Ling's men finished with all guns blazing.
Crewe were in disarray by the time Shane Tudor overlapped down the right and tucked in a low shot inside the near post with keeper Williams again failing to get anywhere near it.
Matthews headed a free kick past the far post and Lowe flashed an effort wide as Crewe mounted a late response, but it was too little too late as they were well beaten by a better organised side.