This poem is using the same pattern multiple time:

Il n’est de charme qu‘en toi même (There is no charm but in yourself)
…
Il n’est clarté que dans tes yeux (There is no light but in your eyes)
…
Il n’est blancheur que sur ton front
…
Il n’est ciel pur que dans ton cœur

Prose French would use il n’y a … que instead of il n’est … que

Il n’y a du charme qu‘en toi-même (There is only charm in yourself)

Il n’y a de la clarté que dans tes yeux

…

One shouldn’t confuse ne pas (not) and ne que (only):

Il n’a pas vingt ans. -> He is not 20 years old (i.e. he is either younger or older than that).

Il n’a que vingt ans. -> He is only 20 years old.

The two-word construct ne … pas is the “basic” way to form a negation in French. The two-word construct ne … que is not really a negation: it means “only”. You can see it as a negation meaning “no other than” or “no more than”, but often other languages would not use a negation.

Je ne peux rester que cinq minutes.   (I can only stay for five minutes.)
Il n’y a du charme qu’en toi-même.   (There is charm only in yourself.)

“Il n’est de … que …” is a variant of “Il n’y a de … que …” that is no longer used in everyday French or even in typical literary French, but is still fairly common in poetry. In English, you might use a negation and but to preserve the poetic phrasing.

Il n’y a de charme qu’en toi-même.   (There is no charm but in yourself.)