Messi has carried off the accolade in each of the last three years, collecting his third award in January.
But Mourinho believes Ronaldo would be a worthy winner when the awards come around again, pointing out that a huge part of Real's Primera Division success this season came due to the remarkable goalscoring feats of the former Manchester United forward.
Although Ronaldo's 46 league goals were not enough to beat Barcelona's Messi to the title of the league's top scorer - known as the Pichichi - they steered Madrid to the title.
And for that reason Mourinho believes his 27-year-old compatriot should be rewarded by FIFA when Ballon d'Or voting takes place.
The Madrid boss told Portuguese TV station SIC: "Cristiano has to win the Ballon d'Or, not because he has been the top goalscorer, he was that already last season, but because his goals have delivered a title.
"Messi scored 50 goals that weren't worth anything, in the same way that Cristiano scored 42 last season that didn't stand for anything.
"He hasn't been able to win the Pichichi and I believe he should be compensated with the Ballon d'Or."
Mourinho described his first league title in Spain as the toughest he has ever won.
The 49-year-old Portuguese has now won seven championships in four different countries after collecting two league titles each with Porto, Chelsea and Inter Milan.
But he believes overcoming Barcelona has been the biggest challenge of his career.
He told Portuguese sport newspaper Record: "All the titles are well recognised, this is undeniable.
"But I can say that this was the most difficult of the seven titles I have won.
"This was more difficult because we had an opponent that is recognised as the best team in the past few years.
"Throughout the whole tournament there was a great pressure because if we drew we could lose points in the title race. For this reason it has been the most difficult, but also very deserved."
Mourinho's team reached 100 points, breaking Barcelona's previous 99-point record.
"The important thing was to win the title, but when we won it and we could get to 100 points, we maintained a high motivation level and went in search of these victories," Mourinho said.
"Madrid has won 32 leagues, but this team will be remembered as the team of 100 points, because at this moment it is a unique mark and, I believe, very difficult to beat."