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MongoDB has a "Two Phase Commits" concept.

Operations on a single document are always atomic with MongoDB databases; however, operations that involve multiple documents, which are often referred to as “multi-document transactions”, are not atomic. Since documents can be fairly complex and contain multiple “nested” documents, single-document atomicity provides the necessary support for many practical use cases.https://docs.mongodb.com/v3.4/tutorial/perform-two-phase-commits/

Since as Schema in GraphQL create separate document, How GraphQL handle this?

GraphQL doesn't have any intrinsic notion of transactions or atomicity. The only statement along these lines is that multiple top-level fields in a single mutation are resolved serially with the expectation that later mutations will see side effects from previous ones. If you have multiple changes in a single GraphQL call and a later one fails, GraphQL says absolutely nothing about whether a first one should be rolled back.

If you're implementing a GraphQL schema in a way that requires changing multiple documents or records, it's up to you as an implementer (or possibly an intermediate library you're using) to provide whatever atomicity and consistency guarantees you need. GraphQL doesn't provide anything here.