The Blues goals were spread around the side, with George McGee, George O'Neill, Corey O'Keefe and Kieran Dunbar all notching one apiece, and one arriving courtesy of a Crewe own goal.
Despite making the better start, Blues actually found themselves behind early on in the contest. But with their good play they were soon back in it as a Crewe player put through his own net.
McGee fired Blues into the lead on the half-hour mark, before O'Neill made it 3-1 to the hosts before the break.
However, Crewe rallied after the restart and scored twice without reply to level the scores.
With the game seemingly heading for a draw, O'Keefe fired Blues back in front, before Dunbar made sure of the victory with a stoppage time goal.
"I imagine it was a good game for the neutral, but not so much for the coaches," said Blues academy coach Steve Spooner.
"We started really well and dominated the early exchanges but then conceded a goal. Despite that the players showed a calmness and stuck to what we'd asked them to do scored twice to go into half-time with a 3-1 lead.
"Crewe came out after the break and got an early goal which rocked us, but then we settled down. They thensneaked another one with about ten minutes left, but we kept with it and scored twice more ourselves late on.
"It was a great team performance overall and they all knew what their respective roles were. We finished the game with three U16s and two U15s on the pitch, which bodes well for the future."