Your sentence is almost correct but needs a small change to sound natural and grammatically correct. The sentence currently is:
Once an echidna has dug itself into the ground, a hungry predator will have only its spines.
To improve it, we can add a word to complete the idea clearly. A better version would be:
Once an echidna has dug itself into the ground, a hungry predator will only have its spines to attack.
Or simply:
Once an echidna has dug itself into the ground, a hungry predator will only have its spines.
Because the phrase 'will have only its spines' sounds incomplete, adding 'to attack' or similar words helps. Otherwise, the sentence is grammatically correct. Also, placing 'only' before 'have' or before 'its spines' is acceptable, but 'will only have its spines' sounds better.