The 19 year-old full-back played in last weekend's clash against Wales, but had a slight problem with his hamstring this week. Morgan has only just returned from a lengthy period out with a wrist injury, and is rested as a precaution.
Elsewhere in the England representative sides, Gloucester's Ryan Lamb starts at scrum-half for England U19s against their French counterparts. The U19s play France on Friday 11 February at Doncaster RFC, kick off 7pm.
Looking ahead to England's U21s clash against the French coach Jim Mallinder said: "Despite the disappointment of last week, the mood has been really positive all week. It's early days yet but things are starting to come together.
"We're delighted with the way we came back to score three tries in the second half last week and our aim this match is to continue our progress and build on that second half performance."
Assistant coach Nigel Redman added: "Falcons hooker Stuart Mackie has been called up to the bench to replace Neil Briggs and Saracens' David Seymour has been selected at open-side flanker on the back of regular performances in the premiership this season."
After a series of good performances for his club Northampton Saints, Paul Diggin makes his international U21 debut in the number 14 shirt. "Paul's performances in the last two Saints games mean he has been selected in this side on merit and he fully deserves this chance to impress."
England U21 team to play France
Friday 11th February, Northampton Saints, kick off 7.30pm
15. Ross Broadfoot, Leicester Tigers
14. Paul Diggin, Northampton Saints
13. Matt Cornwell, Leicester Tigers
12. Simon Whatling, Worcester
11. Tom Varndell, Leicester Tigers
10. Ryan Davis, Bath
9. Ben Foden, Sale Sharks
1. Aston Croall, Saracens
2. David Ward, Bath
3. Matt Hampson, Leicester Tigers
4. Richard Blaze, Worcester
5. Dan Smith, Bath
6. Tom Rees, London Wasps (captain)
7. David Seymour, Saracens
8. Chris Goodman, Bath
Replacements
16. Stuart Mackie, Newcastle Falcons
17. Michael Cusack, Leeds Tykes
18. Tom Ryder, Leicester Tigers
19. James Haskell, London Wasps
20. Lee Dickson, Newcastle Falcons
21. James Wellwood, London Wasps
22. Tom Biggs, Leeds Tykes
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