You might be searching for Battlefield Earth.
The early parts of the book switch between the viewpoints of the human Johnny, and the alien Terl. Both are out searching and meet, and Johnny is riding a horse at the time, which confuses Terl:
Terl didn't know what he was looking at.
He had bunked down in the car in the outskirts. He had the old Chinko map of the ancient city, but he had no curiosity about it.
With a few shots of kerbango, he had eased himself off into sleep, intending to be gone with the dawn, through the city and into the mountains. Senseless, even risky, to go on in the dark.
The car, however, had grown hot with the morning sun before he awoke. And now he stared out at an odd thing in the street before him. Maybe it had been the footfalls that had awakened him.
He didn't know what it was. He had seen horses– they were always falling down mine shafts. But he had never before seen a horse with two heads.
That's right. Two heads. One in front and one in the middle.
And a second animal of similar sort behind. Only this one only had a second body in the middle, as if the second head was bent down out of sight.
Which matches your recollection of the alien thinking the man on a horse was a single weird creature.
The novel is also a very long book.
