Could I list the conference that I didn't attend in the PhD application system even I got my paper accepted?
In general, no. If they ask you to specify a list of attended conferences, then a conference that you didn't attend doesn't belong in your answer, even if your paper was accepted. Claiming that you attended the conference  would be incorrect and could lead to problems if someone found out.

Normally, you should be able to get credit for your accepted conference paper in another category, where you're asked for a list of your peer-reviewed articles. 

However, the form could be designed in a way which neglects the existence of peer-reviewed conference papers. For example, you might be asked for a list for your journal articles only, because the form designers were unaware of fields in which journal articles are not the only kind of peer-reviewed publications. In this case, you should seek contact to the admission committee and ask how to proceed.