GraphQL does not care which database stores your data. MongoDB is a natural fit for many Node.js applications because JavaScript objects can be mapped relatively naturally to MongoDB documents.

A useful architecture is:

GraphQL Resolver
      ↓
Application Service
      ↓
Repository
      ↓
Mongoose Model
      ↓
MongoDB

For example, a resolver should preferably call a service:

const resolvers = {
  Query: {
    user: (_, { id }, context) => {
      return context.userService.getById(id);
    }
  }
};

The service can call a repository:

const getById = (id) => userRepository.findById(id);

The repository can use Mongoose:

const findById = (id) => UserModel.findById(id).lean();

This separation prevents GraphQL resolver code from becoming tightly coupled to Mongoose.

It also makes it easier to replace the persistence layer or reuse the same business logic from a REST API, background worker, or command-line tool.