The reasons for the prohibition of eating milk and meat:

The Mefarshim and Poskim mention several reasons behind why G-d prohibited the mixture of meat and milk:

1. Chok: Some[1] explain that the true reason behind this prohibition is beyond the understanding of a human, and it is hence deemed as a “Chok” [i.e. law that surpasses human intellect] by the Torah.
2. Cruelty: Some[2] explain that eating milk and meat together is forbidden being that it is an extremely cruel insensitive act to cook the meat of the child within its mother’s milk.
3. Idolatry: Others[3] explain that eating meat with milk was the practice of idol worshipers, and thus in order to distance the Jewish people from these practices the above mixture of foods was prohibited.
4. Is like blood: Others[4] explain that eating milk with meat numbs the heart and the soul, just as can be caused upon eating blood. The reason for this is because milk in truth is produced from the blood supply of the body. [The properties of the blood go through a series of chemical transformations and extractions until it become milk. The hormone called prolactin causes the alveoli to take nutrients, such as proteins and sugars from the blood supply and turn them into breast milk.] Now, when one cooks milk with meat it causes that its spiritually damaging blood tendencies become resurrected and is hence considered as if one is now eating blood.
5. Sorcery: In Kabala[5] it is explained that meat and milk have two distinct spiritual roots, and these roots, although individually holy, may not be mixed. Mixing the two together is similar to sorcery, which consists of intertwining the Sefiros and Divine names in ways never mandated by G-d.[6] The exact understanding of this cannot yet be revealed, and it will only be revealed after the coming of Moshiach.

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[1] Bechayeh Mishpatim 19 in his 2^nd explanation; Chinuch Mitzvah 92; Keli Yakar

[2] Rashbam Vayikra 11

[3] Rambam in Moreh Nevuchim 3:32; Even Ezra Vayikra

[4] Bechayeh Mishpatim 19; However, see there that he negates this as being the true explanation, and rather gives an explanation in accordance to Kabala, which is explained next.

[5] Bechayeh Mishpatim 19; Chinuch Mitzvah 92; Keli Yakar

[6] Chinuch

[7] Bechayeh Mishpatim 19