Stone oaks, or Lithocarpus species of Fagaceae are ecologically important canopy trees in the tropical and subtropical forests over East Asia, and the fruits of which are important food sources for insects and vertebrates there. The great fruit morphological variation of this genus represents two fruit types, acorn and enclosed receptacle fruit types. However, the evolutionary mechanisms of differentiation into these two fruit types with contrasting morphology remain a puzzle. To reveal the morphogenetic properties of two fruit types, we observed tissue differentiation and development among 20 Lithocarpus species from fruit set to maturity. Unlike in fruits of Quercus, the endocarp differentiation in Lithocarpus fruits occurred later than exocarp and mesocarp. Cupules provided further protection of developing seeds, particularly of acorn-type fruits. Fruits of Lithocarpus and Quercus acorns share similar insect predators. At fruit set, both acorn and enclosed receptacle types were largely identical, with similar tissue morphology and the sequence of differentiation. The distinct difference between two fruit types at maturity came from varied rates and degrees of development between the pericarp and receptacle tissues. We found that heterochrony between two tissues could create substantially divergent ecological strategies for protection and dispersal of their seeds, which is essential for the evolution of two fruit types.