Crocker will move to The FA later this year to start work as Head of Coach & Player Development, a senior position created under the new FA Strategic Plan.
Matt, who has been at the Club for the past seven years, was headhunted as a result of his fine work in helping to establish the Saints Academy among the most prolific producers of English footballing talent.
The Welshman will work with new Director of Elite Development Dan Ashworth, andwill be responsible for The FA's contribution to the Elite Player Performance Plan.
Last June, the Saints Academy became one of the first to achieve Category One status under the EPPP in recognition of the quality of its facilities and the number of players who have progressed to first-team level.
Matt will assist in the recruitment process for his successor and will ensure that a full handover period is completed before he departs to apply his expertise on a national level.
Executive Chairman Nicola Cortese commented:
"Matt will leave us with the best wishes of everybody associated with the Club. He has given Southampton seven years of hard work and dedication, and played an important part in developing the Academy that we have today.
"Although we are sad to lose a talented member of staff, it is an honour to see the work of a Southampton employee recognised by The FA. We are ranked as the best Academy for producing players for the English national teams, so it is no surprise that they have turned to Matt for this vital role.
"We will take great pleasure from seeing a former Saint working for The FA and know that he will be a great asset to the future development of English youth teams.
"The vision that we have initiated at Southampton over the past four years has been imprinted on Matt and, by carrying those principles with him, he will guarantee the future success of English football for years to come.
"Matt will be hard to replace, but we expect serious interest from exceptional candidates who will be desperate to work for an Academy with a reputation such as ours."