While the flamboyant batsman was also named captain of both ICC Test and ODI teams, Test opener Gautam Gambhir too got top billing as he bagged the Test player of the year award.
The ODI team, led by Dhoni, also has dashing Virender Sehwag and the charismatic Yuvraj Singh, whereas the Test team comprises batting maestro Sachin Tendulkar and Gautam Gambhir.
Dhoni played 24 ODIs in the voting period from which he scored 967, inclusive of nine fifties, at an average of 60.43, the strike rate being 86.63.
The Indian skipper beat strong competition from team-mates Yuvraj Singh and Virender Sehwag, and West Indian Shivnarine Chanderpaul.
Australian right-arm fast bowler Peter Siddle was named Emerging Player of the Year.
The 24-year-old Siddle, who made his Test debut against India at Mohali in October last year, has taken 49 wickets in his 12-match Test career.
His 5 for 21 against England at Leeds in the Ashes series this August was his best.
The most coveted Cricketer of the Year award, however, went to Australia's Mitchel Johnson, who had a phenomenal year with both the bat and the ball in Tests and ODIs. Johnson beat Dhoni, Gambhir and England captain Andrew Strauss in a four-way race.
Sri Lanka's Tillakaratne Dilshan was chosen for the Twenty20 International Performance of the Year award for his outstanding performance of 96 from just 57 balls against the West Indies in the semi-finals of the Twenty20 World Cup in England on June 19.
Ireland's William Porterfield was named the Associate and Affiliate Player, while New Zealand got the Spirit of Cricket award.
Aleem Dar got the Umpire of the Year award.
The awards were given for performances between August 13, 2008 and August 24, 2009.
The nominations were made by a five-member selection panel, headed by former West Indies captain Clive Lloyd. The panel also included former cricketers Anil Kumble, Mudassar Nazar, Bob Taylor and Stephen Fleming.
ICC Test Team of the Year: Gautam Gambhir (India), Andrew Strauss (England), AB de Villiers (South Africa), Sachin Tendulkar (India), Thilan Samaraweera (Sri Lanka), Michael Clarke (Australia), Mahendra Singh Dhoni (India, captain), Shakib Al Hasan (Bangladesh), Mitchell Johnson (Australia), Stuart Broad (England), Dale Steyn (South Africa), 12th man: Harbhajan Singh (India)
ICC ODI Team of the Year: Virender Sehwag (India), Chris Gayle (West Indies), Kevin Pietersen (England), Tillakaratne Dilshan (Sri Lanka), Yuvraj Singh (India), Martin Guptill (New Zealand), Mahendra Singh Dhoni (India, captain), Andrew Flintoff (England), Nuwan Kulasekara (Sri Lanka), Ajantha Mendis (Sri Lanka), Umar Gul (Pakistan), 12th man: Thilan Thushara(Sri Lanka).
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