Evolution of aquaculture is essential to supply the need and meet the demand for aquatic-based protein due to increasing global population and increased market demand. In the last decades, the shrimp sector has been considered one of the fastest growing aquaculture systems due to its economic significance. Growing efforts have been made to increase the production of cultivated shrimp through the development of aquaculture practises. However, in high-density shrimp farming, shrimp has been threatened by frequent diseases and several environmental stressors which results in significant variations in shrimp survival rates. Thus, understanding the driving environmental and managerial factors that affect shrimp health may support the global efforts for promoting sustainable shrimp aquaculture. A distinct intestinal microecosystem that the host’s microbiota can create is intimately linked to the host’s ability to survive, grow, and develop. The intestinal microbiota of shrimp is in a state of dynamic equilibrium under normal circumstances to preserve the intestine’s typical physiological functioning. Shrimp has high diversity and dynamic composition of gut microbiota including Proteobacteria, Bacteroidetes, and Actinobacteria. There is a high correlation between the development of shrimp intestinal microbiota and environmental changes and subsequently the health status of shrimp. This correlation seems to be highly plasticity, even over short-term timescales. The changes in aquaculture ecosystem across age, environment, diet, and diseases or the exposure to new habitat has a great impact on composition of shrimp microbiota. This review summarizes the methods of shrimp aquaculture and the impacts of ecological factors (e.g. dietary manipulation, age, physiological development, and other environmental factors) on gut microbiota composition as well as the intervention approaches to modulate the intestinal microbial composition.