what are you trying to do? the problem with your code in there is that you are not providing all the required fields of the employee entity - phone is missing

orm.em.create(EmployeeRecord, {
  id: 1,
  employee: { user: 5, phone: '123' },
});

also you are trying to create the very same entity twice (EmployeeRecord with ID 1), so the second insert query fails.

right, now i get it. well, you cant use em.getReference() without knowing the PK, if that's not clear yet. the PK is present after the first flush.

i am still not sure what you are trying to do, but it feels like you expect to be able to do things without knowing the FK value. you cant.

Let me explain:
First, I create a Employee in database, means that there is an employee whose name is "Foo" and phone is "12345":

  const newUser = orm.em.create(User, { id: 5, name: "Foo" });
  orm.em.create(Employee, { user: newUser, phone: "12345" });
  await orm.em.flush();

Then in some cases I want to save the records (For example: log-in record) of the Employee to EmployeeRecord.
Another way is to execut await em.findOne(Employee, {user: {id: 5}}) first, but I want to skip this, cause I already know the Employee PK is {user: {id: 5}}:

  orm.em.create(EmployeeRecord, {
    id: 1,
    employee: { user: orm.em.getReference(User, 5) },
  });
  await orm.em.flush();

Wow! That's it!
Now I understand, I had read the doc from https://mikro-orm.io/docs/composite-keys , tried [PrimaryKeyProp]?: ['user'] and failed.
The key is: In my situation [PrimaryKeyProp] should not be an array!
Thanks so much!