The honey bee is a highly eusocial insect. Generally, a healthy colony is made up of a queen, workers and drones. Despite being genetically identical, the queen and workers show striking differences in morphology, behavior, and lifespan. Many studies have suggested that the main factor leading to caste differentiation is nutrition, which can cause differential expression of a large number of genes and proteins between queen and worker larvae. With the development of epigenetics, there have been new insights into the regulatory mechanisms of gene expression, that is, DNA methylation, and the correlation between noncoding RNAs regulation and histone acetylation with the regulation of gene expression. These new insights also provide a new theoretical basis for caste differentiation in the honey bee. This article reviews the progress of epigenetics and caste differentiation in honey bees.