In this research, a stratigraphic section of carbonate rocks of Qaleh-Dokhtar Formation (Middle-Late Jurassic?) with 306.3 m thickness located in north of Qayen city, Southern Khorasan Province, has been measured and studied. This sequence has been made of thin to thick and massive layers of limestone, dolomite, sandstone, shale and marl. Based on both field and laboratory studies, totally 11 carbonate microfacies and 2 clastic petrofacies were determined which have been deposited within four coastal, lagoon, barrier and open marine facies belts within a rimmed-shelf type carbonate platform. The most significant diagenetic processes which have been observed in Qaleh-Dokhtar Formation samples are cementation, compaction, formation of various types of porosity, dissolution, neomorphism and replacement. Interpretation of paragenetic sequence of the studied limestones reveals the effects of diagenetic processes in marine, meteoric, burial and uplift stages. Geochemical studies of elemental analysis show that the palaeoenvironment of formation of these deposits has had similar to the recent semi-tropical regions. Furthermore, the diagenetic environment of these carbonate rocks has had a semi-closed to closed geochemical system.