Why did the north have more large cities than the south?

Because most of the industries were established in the North, whose economy was largely based upon the production and trade of industrial products, while the economy of the South was mostly based upon monoculture and crops developed by slaves' labour.

Therefore the North needed a massive employment of more and more specialized manpower, which had to live in the vicinity of the factories, thus growing the size of the cities.

The South needed instead more and more land to exploit its agricultural production.