In Japanese, “what do you mean?” is “どういうこと（ですか）？’ or “どういう意味（ですか）？”
Dooyuu koto (desuka)?
What do you mean? (What do you want to say?)
Dooyuu imi (desuka)?
What do you mean? (What does it mean?)
If you add “desuka”, it will be the polite form.
Those questions may ask what someone means or what someone talks about. You can also use them when you don’t understand their content or their opinion, not only when you don’t understand their Japanese.
When you learn Japanese, you want to ask “what does this word mean?” pointing to a specific word. In that case, you can say,
XXX wa dooyuu imi desuka?
What does XXX mean?
Or, you could say,
XXX no imi wa nandesuka?
What is the meaning of XXX?
意味（いみ imi）means “meaning”. You can also ask a similar question without “意味”.
XXX wa nandesuka?
What is XXX?