The top-ranked Spaniard is on course for a record-extending 11th Monte Carlo title.
Thiem, an Austrian who is seeded fifth and beat Nadal twice before on clay, earned sympathetic cheers from the crowd when he finally won a game in the second set.
“It is not a normal result. He played the last two semifinals of Roland Garros,” Nadal said. “He’s one of the best players in the world, especially on clay.”
However, the typically modest Nadal praised himself a little, too.
“I played great. I played so well this afternoon, playing very aggressive, backhand, forehand, serve. I’m defending well, returning well,” Nadal said. “It is difficult to play better than today. Being honest, I have to recognize that.”
Nadal recently returned from a right hip injury, which forced him to retire during the Australian Open quarterfinals. The problem then flared up again, and he dropped out of the Mexico Open and Masters tournaments at Indian Wells and Miami.
But since coming back in early April, Nadal has not dropped a set in five straight wins, including two in singles for Spain in the Davis Cup. He needs to win this tournament to keep his No. 1 ranking, or it will go back to Roger Federer.
“The Davis Cup probably helped to come here with better rhythm, better confidence,” Nadal said. “But, of course, things are going much better than what I thought two weeks, three weeks ago. That’s the truth.”
Nadal will next face Grigor Dimitrov, who may prefer not to think too much about their head-to-head rivalry: 10-1 to Nadal.
The fourth-seeded Bulgarian beat No. 6 David Goffin 6-4, 7-6 (5) in an error-strewn match.
Goffin led 4-0 in the second set but the Belgian missed three set points at 5-4.
Nishikori, feeling his way back into tennis after a right wrist injury deprived him of playing in the last two majors, served for the match at 5-4 in the second set. Cilic, the Australian Open runner-up when the Japanese player was still recovering from a torn tendon, saved three match points and then won the tiebreaker in style.
But the big-serving Croat, who needed a few minutes of massage treatment on his sore and bandaged right knee, faded in the third set as the heat lessened.