The lively 16-year-old tucked home a 52nd minute penalty, a minute after Chris Maguire had given his team the lead.
Goodwillie then nodded home a fine third 18 minutes from the end.
Chances were scarce in the opening half as the older Jersey team fought valiantly to keep the Scots at bay.
Jersey’s centre backs Joel Speight and Tom Poole turned in good performances in the half supported well by full-backs Danny Hughes, who used the ball well, and Sam Dewhurst.
Jersey goalkeeper Jack Jouanny, who was fooled by Goodwillie feigning to shoot, recovered well to make the only notable save of the opening half.
Defences were on top and despite both sides playing good possession football each appeared to lack someone to craft an opening.
But that changed when Scotland, who are preparing for European Championship matches in Hungary in October, upped their pace after the break.
James Henry made a fine run down Jersey’s right early but unfortunately nobody met his cross which flew across the face of goal.
Minutes later Andrew Shinnie provided a similar cross but this time Maguire was on hand to tap Scotland ahead.
Goodwillie, a tricky forward with quick feet, exchanged passes with Maguire on the end of Jersey’s area and racing into the box he was fouled by Joel Speight – penalty.
Goodwillie sent Jouanny the wrong way to make it 2-0 and with Scotland dictating matters Jersey, who worked hard but were kept at bay by some fine defending by Ross Hamilton and Jamie Laird, conceded a third when Goodwillie got ahead of his marker to powerfully nod home a free kick from ten yards.
Ross Mathie, Scotland’s youth team coach, said: ‘The Jersey lads gave us a good game, it was just what we were looking for.
First half they played very well but we increased the pace in the second half and Jersey tired.
‘I’ve got a headache now as seven regulars were unable to make the trip and the fringe players who have come in played well.
That’s given me plenty to think about.
Full report in today’s JEP.
