Ricky Duncan's side was two down before the game had got into it's stride with Rowan Murray beating Blues keeper Ian Joyce twice in the opening minutes.
One of the three United players with first team experience, Johnny Herd, pulled one back with a spectacular 30-yard strike but Jamie Peters restored the Suffolk club's two goal advantage and the game was as good as settled just before half time when Reggie Lamb headed home.
Rhys Henry did lob Ipswich shot stopper Ian McLoughlin just after the break to give Blues a sniff of a comeback but with Lambe completing his hat-trick around the hour mark, the score was now an unbeatable 6-2 to the home side.
There was still time in the last quarter for Rhys Henry to hit home a Justin Hazell cross and Billy Clarke to grab Town's seventh.
All in all a sobering experience for the youth team players involved who have to get back to the serious stuff of trying to win the Alliance League title on Saturday away to Rushden & Diamonds.
Southend United: Joyce, Owinja, Herd, Abbey, Whittikar, Reynolds, Hazell (Ngoo 72), O'Keefe, Calver, Henry, Forshaw.
Subs not used: Merrick James-Lewis, Masters, Stevenson, Osifuwa.