In order to explore the genetic regulation mechanism of citrus fruit size and mass, mapping analysis of quantitative trait loci (QTLs) of fruit size and mass was carried out to find regulatory genes. The segregating population in this study was the F1 generation with a total of 94 plants, from the cross of ‘Wanmi 2’ [Citrus unshiu (Mark.) Marc.×C. sinensis (L.) Osb.] and a local sweet orange cultivar ‘Licheng 2’ [C. sinensis (L.) Osb.]. Conserved ortholog sequence (COS) and simple sequence repeat (SSR) markers were used to construct a genetic linkage map of the segregating population. Fruit size and mass were measured at the full maturing stage. Genetic transmitting ability analysis and QTL mapping were carried out. The results showed that this study constructed a genetic linkage map, which contained 201 markers, 10 linkage groups, with a total length of 1 194.5 cM. Four QTLs related to citrus fruit mass, three QTLs related to citrus transverse diameter, and four QTLs related to citrus longitudinal diameter were detected. All the QTLs were distributed on WL3 and WL8 linkage groups. A batch of functional genes (GATA transcription factor, auxin response factor and GDSL esterase) related to the development of citrus fruits were identified according to the functional annotations of the genes in the genome defined by the markers. The QTLs located and the candidate genes identified in this study will be helpful for citrus breeding and theoretical research.