Hi Keiko,
When we emphasise the fact that someone or something is famous for a particular quality, we use "known for".
Example: Japan is known for cherry blossoms.
When we want to associate someone or something with another label, we use "known as".
Example: Rowan Atkinson is known as Mr Bean.
In your example, Kyoto was an ancient capital of Japan.It is a label (capital) which we ascribe to Kyoto.
Hence, we use " known as".
In contrast, Kyoto is "known for" its beautiful temples. Now, Kyoto is famous in many people's minds for a quality -- beautiful temples.
Hope this helps.
Cheers,
Lance