Hi Hui
The previous answers have all highlighted different problems with the 3 sentences.
My interpretation is this:
1) It is time that we went home.
It's ok, except that you would only normally encounter this sentence in reported/recorded speech and the 'that' would normally be dropped for brevity and clarity:
"It's time we went home."
This effectively means that the appropriate moment has arrived when we should go.
2) It is time that we should go home.
Not correct. To be reasonable English, you will need to replace 'it is time' with 'now':
Either: "Now we should go home", or "We should go home now".
If 'now' is at the beginning of the sentence, the emphasis is that going home is the next thing we should do. If it is at the end of the sentence, the emphasis is that the time to go is right now, at this moment.
3) It is time that we go home.
The tense of the verb 'to go' is not correct here. Use it like this and it is OK:
"It is time to go home." or "It is time for us to go home."
So, once the English is corrected, the answer to your question is that all three have slightly different meanings.
1) is slightly less forceful than 3), but probably interchangeable with it.
2) has one of two slightly different meanings, depending on word order.
3) is a clear and unambiguous statement of fact (the time to go is now).