欧足联官方确认，梅西三次获得欧冠冠军 - 哔哩哔哩

https://www.uefa.com/uefachampionsleague/news/0242-0e97e0ac1cb3-eef786ff788c-1000--messi-all-his-records/

Messi has won the Champions League three times – in 2009, 2011 and 2015 (all with Barcelona). He was also a regular for the Spanish club when they won the trophy in 2006 but was not part of their squad for the final.

欧足联认可梅西三次获得欧冠冠军，虽然巴塞罗那在2005-2006赛季拿到欧冠冠军的时候，梅西已经是巴萨俱乐部的一员。但是梅西没有出现在2005-2006赛季欧冠决赛的巴萨名单中，因此欧足联不认可梅西拿了2005-2006赛季的欧冠冠军。

因此梅西职业生涯是三次欧冠冠军。