I'm Alex, with the Shopify team!
There isn't currently a way to limit the payment options in your store - if it's a payment option that you've set up to offer to your customers, it'll always appear in the checkout. There are some ways that you could communicate this to your customers, however!
You can indicate that a particular payment option isn't available for orders under that amount on your product pages or by adding a note to your cart page, potentially by use of a terms and conditions checkbox. If this is a manual payment method, you're also able to add instructions and general information that will display in the checkout!
Hope that's helped! Please feel free to let me know, and you can always give us a call or start a live chat at any time. We're open 24/7 for your convenience and always happy to assist!
Alex | Shopify