The evolution of Jurassic carbonates is globally significant for understanding the depositional framework, diagenetic phases and sedimentary characteristics of shallow marine shelf deposits. For this purpose, two outcrop sections of the Jurassic carbonates with a road distance of 121 km in the Trans Indus Ranges, NW Himalayas, were included in this study. Geological fieldwork was conducted for sedimentological data, and representative samples were collected for microfacies analysis and diagenetic evolution complemented by carbon and oxygen isotope analysis. Results show that eight microfacies were identified in both sections where mudstone microfacies was only present in the Chichali section, whereas wackestone and packstone facies widely existed in both sections. The diagenetic evolution interpreted that dolomitization and stylolization were pronounced in the Paniala section, while micritization and calcite cementation were prevalent in the Chichali section. The interpreted depositional setting implies the wide range from supratidal to outer ramp shallow marine for the Chichali section, suggesting a wide range and relatively deeper environment, alongside merely intertidal to middle ramp settings for Paniala section. Diagenetic evolution suggests marine to meteoric influence in the Chichali section, while burial and uplift phases were dominant in the Paniala section. The diagenetic events were also validated by the isotopic analysis, where most of the samples with values up to −4‰ VPDB δ18O, corresponding to a carbon isotope range of up to +4‰, were interpreted as the burial phase of diagenesis; meanwhile, a few samples with −2 δ13C and −7‰ VPDB δ18O isotope signatures were marked as meteoric influx in the Paniala section. This study indicates the diversity of the depositional environment and diagenetic heterogeneity by integration of thin sections using isotope data, which are quite applicable to shallow marine carbonates.