Grammarian explains
IT'S (HIGH) TIME + PAST SUBJUNCTIVE
It's (high) time + past subjunctive expresses that something should be done and that it is already a bit late:
- It's time you went to bed. You'll have to get up early tomorrow.
Cambridge does not call it past subjunctive, but past verb.
CAGEL (p. 1004) says about the construction IT BE TIME:
- (i) It is time [you were in bed]. [present state]
- (ii) It is time [ we repainted the house]. [immediate future occurrence]
Here, [i] is straightforwardly counterfactual: "You aren't in bed but you should be".
Example [ii] entails that the situation is not yet in progress: "We aren't repainting the
house, but should do so". A perfect, as in
- It is time you had finished it,
is interpreted as a modally remote version of the present perfect: "You haven't finished but should have
done".
If you are too unfamiliar with this tense use, you can go around it by saying
It is time to clean your room.
Only that in this sentence, the agent of the action of cleaning becomes ambiguous: it can be you, we, they..., depending on context. Also, you lose the warning tone of the mom-speak :)