Morrison made his Under-21s debut in last week's 4-0 win at San Marino and quickly made an impression in front of home supporters, opening the scoring inside two minutes after fine work by Wilfried Zaha down the left.
Lithuania were struggling to get to grips with Morrison, whose flurry of stepovers and dragbacks ended up in a free-kick at the edge of the box from which James Ward-Prowse scored his first goal for the Young Lions.
Gareth Southgate's side went further ahead in the 63rd minute when Saido Berahino netted his third goal in as many appearances, before Morrison came to the fore again.
Having won possession just inside the Lithuania half, the livewire midfielder burst between two defenders before fooling the goalkeeper with a stepover and slotting into the empty net.
Man-of-the-match Morrison was denied the chance of a hat-trick as Berahino netted from the spot in the 76th minute, although did not seem too annoyed as he applauded the West Brom striker's second.
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