Richard Beale's side took a 2-0 lead before the break, courtesy of goals from Ollie Lee and James Fry (pictured). Eddy Gnahore then sealed the victory with Blues' third goal just into the second half.
Wigan had more of the play in the opening quarter of an hour of the match, but it was Blues who looked the more likely side to score.
Theo Bailey-Jones fired just wide for Blues after five minutes, before fellow trialist Scott Hogan tried his luck from distance but he was unable to keep his effort down.
But it was just a matter of time before the hosts opened their account as Koby Arthur slid a precise pass to Lee on the edge of the box and he made no mistake as he side-footed the ball home.
Blues continued to press and the impressive Hogan saw his stinging attempt well-saved by Wigan keeper Marko Marosi.
With ten minutes to go to the break, defender Fry made it 2-0 as he met Lee's deep corner ball with a glancing header that flew into the top corner of the net.
The game was put beyond the visitors with 54 minutes on the clock as Gnahore scored a decisive third goal for his side after Blues broke forward on the counter-attack from a Wigan corner.
However, not content with just a three-goal advantage, Beale's boys continued to press and came close to extending their lead after 74 minutes. Substitute Reece Brown went on a mazy run down the left and beat three players before cutting inside and attempting a brilliant curling shot which rebounded back off the bar.
Hogan was the first player to the ball, but his strike was palmed away by Marosi. A second later the Wigan stopper produced another excellent save to deny Lee from point-blank range.
Wigan continued to struggle against a well-organised Blues defence and the closest they came to scoring a consolation goal was deep into stoppage time when Joseph Johnson smashed the ball against Nick Townsend's bar.
Development boss Beale was delighted with the way his side ended their season: "It was a professional job by the boys to win 3-0 and keep another clean sheet in the process," he said.
"We'd asked them to carry on from last week against Derby where they’d won 4-0, by pressing high up the pitch and passing with a purpose. They pretty much did that without quite hitting those same heights.
"But they did the basics well and the hunger and desire was there and they were able to build on that. We asked them if they could see the game off in the first half and they came close by scoring twice. And even when we got a third goal just after half-time we continued to press and we thoroughly deserved the win."
As well as the overall team display, Beale was pleased with a number of individual performances.
"I was delighted to see James Fry get on the scoresheet with a great goal because he’s worked really hard on his heading recently," added Beale. "Every day after training he’s been staying behind and doing extra work. Charlee Adams came on and didn’t lose a header and he's been working on his headers as well recently. These are the type things we do in training that people don’t see but they come to fruition in games.
"When Reece Brown and Liam Truslove went on they both did well, as did Ollie Lee in the centre of midfield who showed grit and determination. He always carries out the message you want out on pitch as well as encouraging others to do the right thing."Blues U21s:
Nick Townsend, Amari'i Bell, Ollie Lee, James Fry, Jack Deaman, Scott Hogan, Eddy Gnahore, Reece Hales (Liam Truslove, 60), Koby Arthur (Charlee Adams, 60), Theo Bailey-Jones (Reece Brown, 68).
Subs not used: Emmitt Delfouneso, Callum Preston.
Goals: Lee (24), Fry (35), Gnahore (54).
Bookings: Lee (65).