The hosts put up a challenging 287, and then bundled out England for 158.
India colts struck in the third over when pacer Kamlesh Nagarkoti removed opener Max Holden (0) with the team score reading 12.
George Bartlett (7) edged to 'keeper Harvik Desai, giving pacer Shivam Mavi his first wicket. Mavi, who was bowling in the right areas, struck again as he cleaned up opener Harry Brook (26) to leave the visitors struggling at 40-3.
Roy took three wickets to play a part in his side's win at the Brabourne Stadium.
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Roy dismissed Woods (19) as the visitors lost their fifth wicket on 89. The left-arm spinner stuck twice as he first cleaned up Tom Banton (4) and then dismissed skipper Matt Fisher (7), leaving the visitors stuttering at 119-7.
Pacer Ishan Porel had the dangerous Delray Rawlins (46) trapped in front of the wicket. Rawlins stuck two powerful sixes and five fours. Porel then dismissed Henry Brookes (3), while captain Abhishek Sharma finished the proceedings by scalping Aaron Beard.
Desai played a variety of shots, including late cuts, sweeps and drives, before throwing his wicket away.
Prithvi Shaw, who failed in the first game, departed for 12 when he was cleaned up by Matthew Fisher.
Rana, the last match's centurion, added 82 runs for the second wicket with Shubham Gill. Gill (24) was the second man to be dismissed with the scoreboard reading 102 for two.