I found out that I have plagiarism in my published journal papers, what should I do now? I published some research papers in an ISI Journal during the past years. But due to the lack of precise knowledge of the correct referencing, and particularly due to attending an “unintentional plagiarism class” in my university, perhaps in some places of my papers, referencing rules unintentionally do not meet correctly and exactly. It seems that I have to modify some parts of my papers if possible.
Also in some parts of my papers I commit an intentional plagiarism.
Now what should I do? Should I contact the editor of the journal? Do they reject or retract my papers? I am a PhD student and if my papers are rejected or retracted I could not defend my PhD thesis.

Please guide me. I'm afraid of expulsion from the university and loss of honor.
The journals need to be contacted, but I would not do it directly. Hopefully your university has someone, ideally a committee, who deals with academic misconduct. I would approach this panel with a detailed list of the occurrences in the papers where you now believe you have plagiarised. Explain to the committee how you were unaware of the norms of good academic research practice until your recent class on the topic. Have in place a plan that will help you continue your training and demonstrate to them that it will not happen again. While they may expel you, I think most academic misconduct panels would look favourably on a student who comes forth on there own with a plan in place. The committee should then be obliged to bring he matter forward with the presses and will negotiate a settlement.

As for loss of honor, it sounds like you plagiarised because you did not understand the norms. While some people will hold this against you, more will look favourably on your ability to admit a mistake.