The Otsutsuki Clan is the most powerful in Naruto overall. Each member is mighty and has unique abilities. With their centuries of fighting and life experience, most of them are incredibly intelligent compared to the average Shinobi in Naruto. However, some Otsutsuki are portrayed as more intelligent than others.
Note: This list is based solely on the author's opinion and contains spoilers for Naruto and Boruto.
All primary Otsutsuki Clan members in Naruto ranked based on their intellect
9) Kaguya Otsutsuki
Many fans view Kaguya as a mindless brute. Her fighting ability is abysmal, but her immense power makes up for this. She was able to overwhelm Team Seven by using Amenominaka, Yomoto Hirasaka, and the Hair Binding Technique. Although she may not be brilliant, Black Zetsu used its intelligence to aid her as much as possible in the battle.
8) Urashiki Otsutsuki
Urashiki was sent to assist Momoshiki and Kinshiki in gathering all the chakra on earth and creating a chakra fruit. Although he was a low-ranking member of the Otsutsuki Clan's main family, Urashiki was probably the most arrogant. This arrogance caused him to create incredibly unwise decisions, especially during his fight against Naruto, Boruto, and Jiraiya.
7) Kinshiki Otsutsuki
Kinshiki was Momoshiki's initial teammate and foster father. Throughout his time in Boruto, he was only shown following Momoshiki's orders. He could never give a good display of his accurate intelligence, but he struck many fans as somewhat intelligent as he was proficient in using many different weapons. Kinshiki was also able to take on the Five Kage, which requires both brains and brawn.
6) Momoshiki Otsutsuki
Momoshiki was the head of the Otsutsuki trio, consisting of himself, Kinshiki, and Urashiki, who was sent to obtain the Tailed Beasts' chakra and cultivate a chakra fruit. Although incredibly arrogant, he could predict many of the actions that both Sasuke and the Five Kage made during the fight. Momoshiki also showed excellent proficiency in Ninjutsu, Taijutsu, and various Rinnegan.
5) Ashura Otsutsuki
Although Ashura was not as bright as his older brother initially, he proved his intelligence later on. He is the progenitor of the Uzumaki and Senju Clans and inherited Hagoromo's teachings of ninshu after Indra's display of darkness. He was also capable of using each of the basic Nature Types and many more. This allowed him to create some incredibly powerful Jutsus such as Amenomihashira and Six Paths: Kunitsukami.
4) Indra Otsutsuki
Indra is Hagoromo's eldest son and the Uchiha Clan's progenitor. He used his father's ninshu teachings to mold chakra and formed modern-day ninjutsu. Because of Indra, there are a vast amount of different techniques that Shinobi can use in combat. He was also incredibly skilled in Kenjutsu, as he could take down opponents with both a regular katana and his Susanoo blade.
3) Hamura Otsutsuki
The younger twin brother of Hagoromo, Hamura, is also brilliant. He could use every primary Nature Type in the show and create a way for Kaguya to be sealed for centuries. After this, he decided to live on the moon to watch over Kaguya and started his clan of Moon Otsutsuki. This led to the creation of the Hyuga Clan.
2) Isshiki Otsutsuki
Isshiki Otsutuski was the newest Otsutsuki Clan member to be introduced to Boruto and acted as the leader of Kara. He was also the strongest villain to date in the Naruto series as he was able to take down a full-powered Naruto and Sasuke without breaking a sweat. Using his intellect, he was able to form an organization of compelling individuals and pursue his goals, all without being discovered by the significant Shinobi villages.
1) Hagoromo Otsutsuki
Hagoromo Otsutsuki is the Sage of Six Paths and the creator of ninshu. He and Hamura figured out a way to defeat their mother, Kaguya, who was essentially immortal. He was also able to create the Tailed Beasts using the Creation of All Things Technique. Hagoromo was also able to use his immense intellect to invent his own Sage Mode and various Jutsus.