There are many factors that allowed the Spanish to conquer the Inca Empire. Let us look at three that are emphasized by Jared Diamond in Chapter 3 of his book Guns, Germs, and Steel.
First, the Spanish succeeded because of their superior technology. The Spanish had guns, but they also had things like steel weapons and steel armor. The Incas did not have anything that was nearly strong enough to penetrate Spanish armor or shield them against Spanish weapons. Therefore, the Spanish had military strength out of all proportion to their numbers.
Second, the Spanish succeeded because European germs had devastated the Incan Empire prior to the Spanish attempt to conquer it. The Incas, like all natives of the Americas, had no resistance to Eurasian infectious diseases like smallpox. This allowed those diseases to kill large numbers of Incas, including their emperor. This weakened them greatly.
Finally, the Spanish succeeded because they had writing. The men who went to conquer the Incas had read about how other Spaniards had conquered the Aztecs. They had ideas about how they could defeat the Incas from that. The Incas, by contrast, had very little information about the Spaniards because they could not get written reports from other people who had encountered them. This put the Incas at a disadvantage because they did not have much of an idea as to what the Spanish were capable of militarily or how they were likely to behave.
All of these factors, and more, contributed to the Spaniards’ ability to conquer the Incas.