Crying at work is undignified and unprofessional. Once in a lifetime would be too often, never mind twice in a year.
The organisation doesn't seem to value you as an employee, possibly due to poor performance or you not fitting in with the corporate dynamic. Presumably, your manager has told you what the problem is and that is why you cried.
If that is the case, what can he do? If you want him to reverse a decision or back-pedal on criticism of your performance, because he "made you cry", you are going to be disappointed.
He could express sympathy that you are upset, but that isn't going to help much in the long-term. If he feels you are using your tears as a weapon, he is more likely to be unsympathetic.
From the limited information you have provided, I suspect they are trying to get rid of you. If that is the case, it is obviously not the right job for you and your situation will become more difficult (and the occasions when you feel like crying more common) until you are forced to leave.
If you feel you are being treated unfairly or discriminated against, you could seek legal advice.
Otherwise, think your best course of action is to start looking for job that is right for you, where you can do a good job, fit in and be happy. They you can resign with your dignity intact and move on.
And resolve not to cry in front of your new employer.
Good luck.