The 23-year-old Roy completed his fourth List A hundred from just 77 balls and overall hit two sixes and 16 fours in his 86-ball innings as Surrey reached 303 all out from 39.1 overs before bowling Scotland out for 203.
Tom Curran finished with five for 34 from 6.1 overs and Zafar Ansari four for 42 as Scotland, given a decent start as openers Hamish Gardiner and Freddie Coleman put on 94 inside 18 overs, lost wickets in quick succession in a vain attempt to get close to Surrey's huge total.
Coleman made 53 before he was fourth out at 123, leg-before to seamer Curran, the 18-year-old son of former Zimbabwe all-rounder Kevin Curran. It was Curran's maiden senior wicket, in his second YB40 appearance, and he soon added the scalp of Moneeb Iqbal who was bowled for 16 as Scotland's slide continued apace.
Later Curran returned to bowl Majid Haq, Craig Wallace for a 20-ball 35 and Calvin Burnett to return the best List A bowling figures for Surrey for four years.
Left-arm spinner Ansari's victims were Richie Berrington (one), Calum MacLeod stumped for seven, Scottish skipper Preston Mommsen (nine) and Gordon Goudie for a duck.
Both Berrington and Mommsen were caught by Curran, who thoroughly enjoyed his afternoon in a game that will have no bearing on qualification for the YB40 semi-finals.
Surrey, indeed, were more interested in getting meaningful match practice ahead of Tuesday's important Friends Life t20 quarter-final against Somerset and after winning the toss they saw Roy, Steven Davies and Vikram Solanki take full advantage of an unthreatening Scotland attack.
Davies pulled Haq's off-spin for two sixes in the sixth over and there was also an early maximum for Roy as he raced to fifty from 39 balls. The pair had put on 91 for Surrey's first wicket inside 11 overs when Davies was caught off fast bowler Goudie for 31.
Solanki then hit a six and eight fours in his 63 from 47 balls, adding a further 126 in 14 overs for the second wicket with Roy, who completed his hundred in the 23rd over.
Both Roy and Solanki were caught at long on attempting to hit seamer Burnett into a sparse crowd and the rest of the Surrey innings fell away somewhat, with only Jon Lewis's 20-ball 25, a late six by Gareth Batty and a six-run penalty against Scotland for not bowing their 40 overs within a time limit taking them past 300.
Gardiner, a 22-year-old on his List A debut, pulled Lewis for six and also drove Batty over extra cover for one of his five fours in a promising 48 from 56 balls before being bowled heaving across the line at Batty, and Coleman also batted well for his 53 off 71 balls with six fours.
Some late blows from Wallace and Burnett, though, were all that Scotland could offer as Curran and Ansari carved through the rest of their batting order, and the end came in the 36th over of their reply.