Northern agriculture was based on relatively small farms, that produced and exported food. Before the war corn, wheat, beef, and such were all exported to countries in Europe, particularly England. While the North is often characterized as the industrial side to the South's agriculture, a better way to look at it would be in thirds. South; cash crops, North coast; developing industry, Northwest (now northeast); small food crop farming. Much of the Northern States were still very heavy in agriculture, and a lot of the Northern industry was built to cater to that, with the production of mechanical reapers, planters and plows that let fewer people farm even more land.

Southern Agriculture was instead focused on cash crops, primarily cotton, but also tobacco and indigo. The plantation system used in much of the South encouraged mass growing of profitable resources, with the land unsuitable for cash crops used to grow food.

As the war broke out, the North still had access to it's overseas markets, and a new market with the Federal Government buying up food to feed the troops. Meanwhile, the South continued to raise cash crops, with little effort devoted to switching to food growing, despite the South having no access to foreign markets, to either sell their crops, or buy food, which they could no longer buy from the North. Meanwhile, the Northern population advantage and wealth actually expanded the agricultural base. I mentioned the cutting edge farm tools (for their day) above, but while the North was fielding millions of soldiers, it also initiated one of the biggest land sales in US history, providing hundreds of thousands of families with access to land and equipment to start new farms. Most of this land was sold at rather low prices, and with the still expanding railroad network, these new farmers could move their crops to the coastal ports.

The food vs cotton is also one of the factors that England had to consider in whether or not to intervene. While not a necessarily a major factor, the choice of feeding factories southern cotton, or feeding factory workers northern wheat, and the reaction of said workers if they were told to suck it up.

So: short version.

The northern farmers were already focused on producing food, and had both the resources and political backing to not only increase the land and population available to increase production, but also an increasing technological expertise to increase yields with fewer people, and access to more markets.

The South, focused on non-food cash crops, failed to make the shift to food growth in any meaningful amount, and with their ports blockaded, had no way to import food from elsewhere once their previous major source of food (the North) started shooting back at them.

edit: spelling and grammar.