Tomato is a globally popular vegetable with special flavor and rich nutrition. Along with the increasing need of the customers on the fruit quality, people have paid attention on the sepals, as an important part of fruits. In this study, the genetic populations (P1, P2, F1, F1' and F2) were generated by using tomato genotypes with sepal envelopment and upward curl as parents, respectively. The F2 population was genotyped using 130 polymorphic SSR markers to obtain the genetic linkage map, which contained twelve linkage groups, with a genetic map length of 4682.22 cM and an average genetic interval of 36.02 between markers. The QTL mapping of six sepal-related morphological traits (sepal length, sepal width, sepal thickness, sepal area, sepal upward curl, and sepal upward curl) enabled identifying 20 QTL, of which two were associated with sepal length, three with sepal thickness, 11 with sepal area, four with sepal crimpness. These high-confident QTL at each trait were further analyzed, and might lay a foundation for deciphering the regulation and improvement mechanisms of tomato sepal morphology.