The 30-year-old scored 2,735 runs in 37 matches in all formats last year, averaging 68.37 with 11 hundreds and nine fifties.
In ODIs he scored 1,202 runs at an average of 133.55 and became the fastest player to reach the milestone of 10,000 runs in the format.
Four England players were also named in the ICC’s ODI team of the year for 2018.
However, no England players made it into the Test team of the year, with New Zealand trio Tom Latham, Kane Williamson and Henry Nicholls among those selected, alongside India skipper Kohli, who was named as captain of both the Test and ODI sides.
Wicketkeeper Rishabh Pant claimed the ICC’s Emerging Cricketer of the Year award.
Root said: “It feels really great to be named in the ICC ODI squad and the fact that three of my team-mates are there along with me, makes it extra special.
“We had a fine year and expectations are on the rise as we look forward to playing the ICC Cricket World Cup at home this year.”
Test team of the year
Tom Latham (New Zealand), Dimuth Karunaratne (Sri Lanka), Kane Williamson (New Zealand), Virat Kohli (India, cap), Henry Nicholls (New Zealand), Rishabh Pant (India, wk), Jason Holder (West Indies), Kagiso Rabada (South Africa), Nathan Lyon (Australia), Jasprit Bumrah (India), Mohammad Abbas (Pakistan).
ODI team of the year
Rohit Sharma (India), Jonny Bairstow (England), Virat Kohli (India, cap), Joe Root (England), Ross Taylor (New Zealand), Jos Buttler (England, wk), Ben Stokes (England), Mustafizur Rahman (Bangladesh), Rashid Khan (Afghanistan), Kuldeep Yadav (India), Jasprit Bumrah (India).
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