As a rule of thumb, 1-story homes cost more than 2-story homes of similar square footage. Why?
Using a simplistic example, a 2000 square foot 1-story home will have a larger "footprint" than a 2-story home with 1000 square feet on the main floor and 1000 square feet upstairs. Therefore the 1-story home will have a more expensive foundation and oftentimes requires a larger (more costly) home-site because of the increased width and/or depth.
Similarly, the 2-story home has a roof system to cover the 1000 square foot second floor, while the one-story home requires larger roof trusses, more sheathing, more shingles and more attic insulation.