A secure permanent account password should be complicated, which may also make it hard to remember and keep secret. Even if you do everything right, it's still vulnerable to things like viruses that record your keystrokes or copy your password to a clipboard. The one-time password stops working right away if you don't use it and gets disabled after you log in to Yandex using it. Trying to steal this type of password is useless.
Using Yandex Key, you can log in to your account either with a one-time password only, or with a combination of a permanent and one-time passwords.
Read more about using Yandex Key on the Help pages: