The Oriental fruit moth, Grapholita molesta (Lepidoptera: Tortricidae), is a major pest of tree fruits worldwide, and the diapausing larvae overwinter in cryptic habitats. Investigations of overwintering G. molesta were conducted in adjacent peach, pear and apple orchards in Northern China over three consecutive winters to determine the overwintering site and habitat preferences of the moth. Counts of overwintering larvae in the different orchards demonstrated that the late-maturing peach orchard (‘Shenzhou honey peach’) was the most preferred overwintering habitat with more than 90% of the collected larvae. Larvae were more abundant in host trees, and they very rarely overwintered in the soil. The overwintering site preferences on the host trees were significantly different; over 50% larvae were located in the tree trunks, and followed by main branches. Most of the G. molesta overwintered on the sunny side of the host trees at or below 60 cm from the ground; a few were cocooned on the shaded sides of the trees or greater than 60 cm from the ground. G. molesta began overwintering between August and October, mid- to late September was the peak period for entering winter diapause during 2011–2013 (77.78, 67.59 and 71.15%, respectively). Our findings improve understanding of the orchard habitat and overwintering site preferences of G. molesta and would be useful in the development of efficient forecasting and pest-management strategies for orchards during the winter and early spring.