Syntax has a y where English would otherwise write i, and that is the Greek letter upsilon coming through Latin. It is one of the most useful single-letter clues in English spelling: an internal y that works as a vowel — myth, system, crypt, syntax, hymn — almost always means Greek.
The word is syn-, "together," plus tassein, "to arrange" — a putting in order. English took it about 1600 through French and Late Latin, first in the general sense of a systematic arrangement of parts, and by the 1610s specifically in grammar, for the arrangement of words in a sentence. It was extended to logical systems in 1922 and to computers in 1958, which is the usual fate of a good Greek abstraction: every new formal discipline borrows it again.
syntax (n.) c. 1600, "systematic arrangement of parts;" by 1610s specifically in grammar, "construction of sentences, arrangement of words according to established usage," from French syntaxe (16c.) and directly from Late Latin syntaxis , from Greek syntaxis "a putting together or in order, arrangement, a grammatical construction," from stem of syntassein "put in order," from syn- "together" (see syn- ) + tassein "arrange" (see tactics ). Transferred to logical systems by 1922, to computers by 1958. also from c. 1600
syntax came in through Greek, and its spelling follows that family's conventions.
How that family writes these sounds
| short /i/ in the middle | y, transliterating υ, where a native word would use imyth, system, syntax, crypt |
What gives it away on the page
| y as a vowel in the middle | Transliterates υ. Native words use i here.myth, system, physics, syntax, crypt |