Interpretation of the Houyhnhnms has been vexatious. It is possible, for example, to regard them as a veiled criticism by Swift of the British Empire's treatment of non-whites as lesser humans, and it is similarly possible to regard Gulliver's preference  as absurd and the sign of his self-deception. 

Gulliver loves the land and is obedient to a race that is not like his own. The Houyhnhnm society is based upon reason, and only upon reason, and therefore the horses practice eugenics based on their analyses of benefit and cost. They have no religion and their sole morality is the defense of reason, and therefore they are not particularly moved by pity or a belief in the intrinsic value of life. Gulliver himself, in their company, builds the sails of his skiff from "Yahoo skins." Examples of the Houyhnhnms' lack of passion surface mainly during their annual meeting. A visitor apologizes for being late to the meeting as her husband had died shortly before and she had to make the proper funeral arrangements, which consists of burial at sea. She eats her lunch like all other Houyhynms and is not affected at all by her loss, rationalizing that gone is gone.

A further example of the lack of humanity and emotion in the Houyhnhnms is that their laws demand that each couple produce two children, one male and one female. In the event that a marriage produced two offspring of the same sex, the parents would take their children to the annual meeting and trade them with a couple who produced two children of the opposite sex. 

On the one hand, the Houyhnhnms have an orderly and peaceful society. They possess philosophy and have a language that is entirely pure of political and ethical nonsense. They possess, for example, no word for a lie (and must substitute a phrase — to say a thing which is not). They also have a form of art that is derived from nature. 

After Gulliver makes it out to the shipping lanes he is rescued by a Portuguese sea captain, a level headed individual albeit full of concern for others. The captain's temperament was considered the perfect medium between that of the Houyhnhnms and the Yahoos, and Gulliver had remembered that he was the man he had gotten along best with. When Gulliver returns to England at the end of Gulliver's Travels, he finds the smell and look of his countrymen intolerable. He regards all around him as Yahoos, and he spends much of his time in the stables near his horses, with whom he converses, although he did say he has a friendship with the stable boy due to his love of horses