How to customize order confirmation e-mail
Order receipt emails are powered by Twig templates, just like regular pages. This helps us avoid the inflexibility of tokens and their lack of conditional support ("Only show the Shipping information heading if the token has data"), which were big problems for D7 sites.

You can override the commerce-order-receipt.twig.html template in your theme to customize it.

See https://github.com/drupalcommerce/commerce/blob/8.x-2.x/modules/order/templates/commerce-order-receipt.html.twig