Munro achieved the feat by smashing 104 off 53 balls with three fours and 10 sixes against the West Indies in last T20I at Bay Oval, Mount Maunganui.
With this, the 30-year-old moved ahead of four players, including the West Indies' Chris Gayle, on two T20I centuries.
Bay Oval marked the second century of recently turned opener. Earlier he had scored 101 against Bangladesh in January last year.
Munro's highest score is an unbeaten 109 in the series against India in November.
Munro flying start helped the Kiwis to set a mammoth 244-run target for the Windies.
Martin Guptill also added 38-ball 63 to the side while Tom Bruce (23), Anaru Kitchen (9) and Kane Williamson (19) made short cameos.
New Zealand is already leading the series 1-0, after the second game was washed out on Monday and if the hosts win the concluding match, they will become the top-ranked T20 international team in the world.