Different numbering in appendixes and ToC in LaTeX

I have been struggling with this problem for the past 2 hours. Still no clue. So I am writing this blog post and hope someone can help me.

I use the appendix package to manage appendixes in my dissertation. However, in appendixes, they are numbered as "Appendix A", "Appendix B":

whereas in table of contents, they are numbered as "I, II, III, IV":

I have read the 4-page manual of appendix package many times. But still no clue.

Any idea? Might be some packages conflicting?

PS: During googling, I found a good article though, Writing a thesis with LaTeX.

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