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Circe told him to.
Odysseus chooses to pass by Scylla because, Scylla will only kill 6 men, one for each head. Charybdis will sink the ship, killing everyone. Circe has also advised Odysseus to do choose Scylla. Further, Charybdis is a visible danger, and Odysseus uses Charybdis to encourage his men to pass by quickly. Finally, passing by Scylla and Charybdis is given as the only way for Odysseus to get home from where he is.
Odysseus chose Scylla, and lost 6 men to her arms.
Circe
He plugged the sirens ears and avoided the Charybdis
Sail on the side of Scylla thereby sacrificing only 6 men instead of the entire ship.
scylla and charybdis
Scylla And Charybdis
Odysseus goes through the Sirens by putting beeswax in their ears. Odysseus is tied to the mast while the Sirens are surrounding them and is begging for his soilders to untie him but they don't. He goes through Scylla by just going past it, letting 6 of his men get eaten by Scylla. And he sailed closer to Scylla to get past Charybdis.
Odysseus donned his armor and readied his spear to attempt to fight of Scylla. He then ordered his men to hug the rocks, where Scylla was, as to avoid Charybdis. He was unable to prevent the capture of his 6 men.
Odysseus successfully sailed his ship past Scylla and Charybdis, but Scylla managed to catch six of his men, devouring them alive.
The Sirens, Scylla and Charybdis.