During the first few years the growth of a magnolia tree bush, it is important to prune the new growth branches back to help maintain the circular shape, according to Gardening Guides. Once the bush is well established, simply prune away dead, decaying or infested branches annually. Prune a magnolia tree bush immediately after it finishes blooming in the spring to ensure that the following year's buds are not damaged.
If any branch on the bush does not bloom, assume it is dead, and prune it off, according to Gardening Guides. Cut back any branches that are rubbing against the trunk of the bush or other branches, as this can expose the bark and give way to disease or infestation.
Aim for pruning one-third of the bush all the way back to the ground to encourage new growth from the ground each following year, according to Gardening Guides. Work to remove an even amount of branches from all around the bush to keep it symmetrical. Prune a second time in the summer to cut back on new growth. Focus on removing any branches that have grown excessively longer than others, and trim the bush to a size that fits its space well.