A manuscript critique and a substantive edit are very similar. They both deal with the big picture aspects of a story. They evaluate how well the storytelling elements have been handled and how the work can be improved. This evaluation, in both cases, is delivered in the form of an editorial report.
You may be wondering, if they cover the same topics, what makes them different? Imagine them as nesting dolls. A manuscript critique is nestled inside a substantive edit.
In both cases, you will receive an editorial report analyzing the big picture stuff. But in a substantive edit, you’ll get the editorial report plus notes and edits in the manuscript pages.
What does that mean? Well, while a manuscript critique provides you with a report which points out an issue, explains why it is an issue, and suggests ways to fix the issue, a substantive edit does all of that and flags occurrences of that issue in the actual manuscript.
Simple as that. If you’re still unclear on the difference or want more information, please let me know in the comments.