You can devide your values by 1,000 or 1,000,000
Other way is you can use Waterfall Chart Studio Excel add-in Waterfall Chart Studio
By the way, waterfall charts become the standard type in Excel 2016. But if you use older version of Excel, Waterfall Chart Studio will be useful for you.
You can see how the add-in works here https://youtu.be/Z1pavJW8_e8