Probably from an unused root meaning to enumerate; an assessment (as based upon a census) -- tribute.
Englishman's Concordance
1) computation, proportion to be paid, tribute, tax Part of Speech: noun masculine A Related Word by BDB/Strong’s Number: probably from an unused root meaning to enumerate Same Word by TWOT Number: 1014a
Brown-Driver-Briggs
מֶ֫כֶסnoun masculinecomputation, proportion to be paid, tax (Palmyrene מכסא ReckendZMG 1885, 379 ff.; Late Hebrew מֶכֶס, Aramaic מִכְסָא, tax (hence Arabic as loan-word Frä283); Assyrian miksu, DlHWB 407 (√ מכס); Late Hebrew מוֺכֵסtax-collector; so Assyrian makkasu, compare Arabic ) — Numbers 31:28׳לי׳זַהֲרֵמֹתָ֫ מ and thou shalt separate a tax (duty levied on the spoil) for ׳י, Numbers 31:37; Numbers 31:38; Numbers 31:39; Numbers 31:40; Numbers 31:41 (all P).
Numbers 31:28 HEB: וַהֲרֵמֹתָ֨ מֶ֜כֶס לַֽיהוָ֗ה מֵאֵ֞ת NAS: Levy a tax for the LORD from the men KJV: And levy a tribute unto the LORD INT: Levy A tax the LORD the men
Numbers 31:37 HEB: וַיְהִ֛י הַמֶּ֥כֶס לַֽיהוָ֖ה מִן־ NAS: and the LORD'S levy of the sheep KJV: And the LORD'S tribute of the sheep INT: become tribute and the LORD'S at
Numbers 31:38 HEB:וּשְׁלֹשִׁ֖ים אָ֑לֶף וּמִכְסָ֥ם לַיהוָ֖ה שְׁנַ֥יִם NAS: from which the LORD'S levy was 72; KJV: of which the LORD'S tribute [was] threescore and twelve. INT: thirty thousand tribute the LORD'S both
Numbers 31:39 HEB:וַחֲמֵ֣שׁ מֵא֑וֹת וּמִכְסָ֥ם לַֽיהוָ֖ה אֶחָ֥ד NAS: from which the LORD'S levy was 61; KJV: of which the LORD'S tribute [was] threescore INT: and five hundred tribute the LORD'S and one
Numbers 31:40 HEB:עָשָׂ֖ר אָ֑לֶף וּמִכְסָם֙ לַֽיהוָ֔ה שְׁנַ֥יִם NAS: from whom the LORD'S levy was 32 KJV: of which the LORD'S tribute [was] thirty INT: teen thousand tribute the LORD'S and two
Numbers 31:41 HEB:מֹשֶׁ֗ה אֶת־ מֶ֙כֶס֙ תְּרוּמַ֣ת יְהוָ֔ה NAS: gave the levy [which was] the LORD'S KJV: gave the tribute, [which was] the LORD'S INT: gave Moses the levy offering the LORD'S
tax (hence Arabic 
as loan-word Frä283); Assyrian miksu, DlHWB 407 (√ מכס); Late Hebrew מוֺכֵס tax-collector; so Assyrian makkasu, compare Arabic 
) — Numbers 31:28 ׳לי ׳זַהֲרֵמֹתָ֫ מ and thou shalt separate a tax (duty levied on the spoil) for ׳י, Numbers 31:37; Numbers 31:38; Numbers 31:39; Numbers 31:40; Numbers 31:41 (all P).