A shale lithofacies scheme is commonly used to characterize source rock reservoirs of the Lower Cambrian Niutitang Formation. However, this classification ignores that individual components such as quartz may have different origins, potentially affecting reservoir quality. The main objective of this article is, therefore, to present a refined scheme for lithofacies and an image processing workflow for the detection of quartz types in the Niutitang Formation shales from the Jiumen outcrop in the Guizhou Province (Upper Yangtze Basin, SW China). In order to do so, a combination of bulk density, optical and scanning electron microscopy and image analysis was used. The shale lithology was macroscopically classified into seven major categories and nineteen subcategories. Subsequently, the shales were investigated at the microscopic level, mainly focusing on quartz types and microstructural variations. Afterwards, the workflow to calculate the weight per unit volume (1 cm3) of the quartz types was presented, i.e., firstly, by calculating the weight of mineral matter by subtraction of the measured weight of organic matter from the bulk shale; secondly, by calculating the weight of total quartz in bulk shale from the weight of mineral matter and its proportion calculated from X-ray diffraction data; thirdly, by calculating the weight of detrital quartz and non-detrital quartz with energy dispersive X-ray mapping, image processing and quartz density; finally, by calculating the weight of clay-sized quartz by subtracting of the weight of detrital and non-detrital quartz from the weight of the total quartz. The bulk quartz content was found to be dominated by clay-sized quartz, which may mainly control the mesopore volume available for gas storage and, hence, the shale gas reservoir development.