Insects in temperate climate zones are challenged to endure harsh temperature regimes and the absence of food resources during winter. Many insects overwinter in diapause at different sites. The overwintering sites differ according to the insect species. The study was conducted to investigate the overwintering sites between the two orchard systems for the Grapholita molesta larvae. Overwintering sites of Grapholita molesta were found different between apple grafting systems. More individuals favored the side branches and main bottom trunk as overwintering sites in big tree system (M26) and in dwarf grafting high density system (M9) respectively. There was no significant different between M9 and M26 cultivars in the relative proportion of larvae. However, significant differences were found in the interaction between the overwintering sites and the two M9 and M26 cultivar orchard systems. The natural mortality from the field was estimated as 22.1% and 18.3% from dwarfing, high density orchards and the big tree orchard systems respectively. This study provides valuable information and guidelines to understand the major overwintering sites within different orchard systems for scheduling management actions against spring adult moths population emergence.