Why are the first syllables of “nature” and “natural” pronounced differently?

Solution 1:

As Greg Lee and Peter Shor mention in the comments, the "shortness" of the first vowel in natural /ˈnætʃ(ə)rəl/ can be explained by the concept of "trisyllabic laxing": a stressed vowel in the third-to-last syllable of a Latinate word is often given its short pronunciation even if it is only followed by a single consonant. This also affects the pronunciation of the adjectives national (related to the noun nation) and rational (related to the noun ration).

The pronunciation of nature as /ˈneɪtʃə(r)/ with a long vowel is actually irregular; most of the time, vowels in Latinate words are shortened before a "u" in an (orthographically) open syllable, as Peter Shor suggests in another comment (consider tenure, figure, stature, spicule, ferule). I don't know if there are any details about the history of this word that would explain why it does not rhyme with stature or mature.