Six-time Ballon d'Or winner Messi had informed Barca of his wish to leave the LaLiga club last month, with the Argentina forward hoping to exercise a clause in his contract that would have allowed him to depart on a free at the end of the 2019-20 season.
However, Barca were adamant that option had expired and was not still relevant despite the campaign being extended into August by the coronavirus pandemic.
Manchester City, Paris Saint-Germain and Inter were all linked with a move for one-club man Messi, who eventually confirmed he would stay in Catalonia rather than challenge Barca on legal grounds.
And, though Luis Figo famously made the switch from Barcelona to Madrid, Los Blancos midfielder Kroos does not think either party would have wanted Barca's current star to pull on the all-white kit.
"I don't think so," a laughing Kroos told Blick.
"I don't think the player would be open to coming to Real Madrid. But that's probably mutual. So I don't think that could happen."
Madrid took advantage of the turmoil at their Clasico rivals by winning the 2019-20 LaLiga title, the second time Kroos had won the league in Spain.
The World Cup winner has credited Madrid boss Zinedine Zidane for his work with the club's star-studded squad.
"It helps that he was a great player himself," Kroos added.
"He knows exactly what makes them tick and what it's like to be a Real Madrid player. He applies this knowledge superbly, and he's also incredibly good at managing this group of stars.
"He meets every player at eye level, brings everyone on board and has everything around Real under control. And he is also very good technically. He's the best coach you could ask for."