Microwave ovens are full of mysteries. One of those enigna is the crystal. What its there for beats me? I understand it uses in radio transceivers, tv, oscillators. Why microwave ovens?
Can you show the circuit with the crystal you are asking about?
The magnetron tube in a microwave is a tuned oscillator generating microwaves, but the major tuning element is a properly sized cavity.
It most likely is the oscillator for the microprocessor, both for its normal operation and for the clock/timer.