England led three times but were pegged back, with a late Josip Brekalo goal denying them their only group win.
“We’ve got issues that we need to address with a new team into the next season,” said Boothroyd.
“We’ve clearly got the talent – but talent needs some structure.”
This disappointment comes after elimination for the under-17s at the European Championship in Ireland, which means they will not be able to defend their World Cup title.
Meanwhile, the under-20s finished a lowly ninth in the Toulon Tournament, having won the competition on the three previous occasions. And last year, a 3-0 defeat by Norway meant they missed out on the chance to defend their World Cup title this year.
England U21s were already out of this tournament going into Monday’s game, having lost 2-1 to France and 3-2 to Romania in their first two matches.
Boothroyd added: “Scored six, nine against – they’re not tournament-winning statistics.
“We need a little bit of steel and that’s in our thinking. The teams that we’ve played have been teams that are streetwise, and we’re not. We need to get that into our game all the way through our age groups.”
While England’s attack – comprising of Phil Foden, Demarai Gray, Reiss Nelson, James Maddison and Tammy Abraham – shone at times, the defence was England’s Achilles heel throughout this campaign.
It started well for Boothroyd’s youngsters inside the San Marino Stadium on Monday, when Arsenal winger Reiss Nelson scored from the spot after he had been fouled by Branimir Kalaica.
England should have extended their lead soon after. First, Chelsea’s Abraham fired his toe-poke against the post, then Leicester’s Gray forced a great one-handed stop from Ivo Grbic.
Then came the first jolt. Jonjoe Kenny, who conceded a penalty in the 4-2 defeat by Romania, allowed Josip Brekalo to power past him and he then thundered a strike beyond the reach of Dean Henderson.
England regained the lead just three minutes into the second half – James Maddison, coming off the back of an exceptional season with Leicester, punished Filip Uremovic’s woeful defensive header with a well-placed shot.
Croatia, who looked like they could score with every counter-attack, equalised again just after the hour mark through former Everton player Nikola Vlasic, who fired a 20-yard strike into Henderson’s far left corner.
Then in a game which had already been treated to great goals, Kenny popped up with the best of the lot when he picked up the ball 25 yards out and found the net with a screamer.
However, there was to be one more twist when, with eight minutes remaining, Luka Ivanusec slipped in Brekalo and he fired his low shot past Manchester United keeper Henderson.
The Wolfsburg forward’s goal was the seventh England had conceded in the last 15 minutes of the three group games.