To investigate the differences in nutritional quality of the black rice variety ‘Huamoxiang 5’ under various cropping patterns and compare the advantages and disadvantages between different patterns, we conducted a comparative nutriomic analysis of rice harvested from multiple cropping systems, including monoculture, rice-shrimp coculture, and rice-shrimp-duck integrated farming etc. The study aimed to explore the effects of different cropping patterns on the nutritional composition of rice. The results indicated that the cropping pattern significantly influenced the nutritional quality of ‘Huamoxiang 5’. The nutritional value of whole-grain black rice of ‘Huamoxiang 5’ was significantly superior to that of the polished form. Compared to monoculture, the rice-shrimp-duck integrated farming pattern increased the oil content (P < 0.05) and the levels of B vitamins, soluble phenolic acids, oryzanol, and γ-aminobutyric acid in whole grain black rice, but it reduced the content of protein, starch, vitamin E, anthocyanins, carotenoids, and other substances. This study comprehensively measured the nutritional indicators of ‘Huamoxiang 5’ and demonstrated the differences in nutritional components among different cropping patterns, providing theoretical support for optimizing the rice-shrimp-duck integrated farming model.