Pomegranates bloom in the spring, on buds arising from previous year's growth. Winter is a good time to prune, but how you prune should take into account that if much of the previous year's growth is removed in the winter, very little fruit will be produced that next spring.
Pomegranate bushes should be thinned out to increase sunlight in the interior canopy. Cut entire stalks back to the ground, leaving from 3 to five main trunks that are spaced apart from one another well enough to allow room to enlarge. Allow these trunks to make new growth each season, limiting long whips by tip pruning, and shortening them during the winter if they become too tall for harvesting fruit.
Fertilizer and water are important during the growing season to encourage a balance of fruit production and new vegetative growth each year.