Is there any limit of charging amount for one transaction?

On the API, you can charge from JPY1 for one transaction.
The limit of maximum amount will differ depending on payment methods. 

For the maximum amount for each, please refer to this page.

*Credit card: the payment may not be completed with the amount you requested due to the discretion of the card holder's usage limit or the card company that received the payment request.

*Electronic Money: the limit of the card you own will be the limit that you can charge.