Loquat is an evergreen fruit crop which blooms from autumn–winter, and supports human beings with juicy fruit from late spring to early summer. However, the most traditional cultivars of this crop produce small fruit and bear a much lower yield than its relatives like apple, pear and peach. Large-size cultivars have long been a cherished aim of breeders for improving the production yield of loquat. Agronomic practices like panicle thinning, fruit thinning, growth regulator application, fertilization and so on are easier and more accessible ways for growers to produce large-size loquat fruit on existing production trees. Here, we develop a novel pruning method with an annual double back-cut, which provides vigorous shoot with more leaves and thicker branches for bearing much larger loquat fruit. Cellular observation determined that the vigorous shoot training method motivated cell division to produce larger loquat fruit, and that most of these cell layers were proliferated before the appearance of flower blossoms. Gene expression data of four development stages showed that EjFWL1 and EjFWL2 were notably downregulated in flower buds of the vigorously pruned tree. The data here further confirmed that the cell division capacity during flower development greatly influenced both the flower and fruit size of loquat. More importantly, we developed a novel pruning method to inhibit cell division repressors, promote cell proliferation and enlarge fruit size in loquat.