Young lemon (Citrus limon (L.) Burm. F.) tree with three year old was employed for researching the effects of different pruning modes (light thinning pruning, machinery pruning, heavy pruning) on the fruit yield and its economic benefit. The results showed that the fruit yield of spring-flowering lemon depended on pruning modes, from high to low, the order was light thinning pruning, machinery pruning and heavy pruning, and the economic benefit decreased from light thinning pruning, heavy pruning to machinery pruning in turn. The fruit yield and economic benefit of spring-flowering lemon were consistent. The economic benefits of spring-flowering lemon and the fine-fruit lemon were both declined from light thinning pruning, machinery pruning, to heavy pruning in turn, and the cost of pruning were followed on the order of heavy pruning, light thinning pruning, and machinery pruning. The total benefit was ordered by light thinning pruning, machinery pruning and heavy pruning. From the view of fruit yield and economic benefit, light thinning pruning, as a recommended mode, was the best one, while heavy pruning could seriously influence the fruit yield in the first year.