Over time, stable isotopes have proven to be a useful tool in petroleum geochemistry. However, there is currently insufficient literature on stable isotope geochemistry of the organic elements within shales and crude oils in many petroleum systems around the world. As a result, this paper critically reviews the early and recent trends in stable isotope geochemistry of organic elements in shales and crude oils. The bulk and compound-specific stable isotopes of H, C, and S, as well as their uses as source facies, depositional environments, thermal maturity, geological age, and oil–oil and oil–source rock correlation studies, are all taken into account. The applications of the stable isotopes of H and C in gas exploration are also discussed. Then, the experimental and instrumental approaches to the stable isotopes of H, C, and S, are discussed.