Stable carbon and nitrogen isotopes were used to investigate nutrient pathways and trophic relationships from the rice-crab system in Panjin, Liaoning Province, China. Values of δ13C ranged from −27.38‰±0.44‰ to −18.34‰±0.26‰ and δ15N ranged from 1.10‰±0.88‰ to 9.33‰±0.57‰. Pseudorasbora parva (Stone moroko) had the highest δ13C and δ15N values. The lowest δ13C values were obtained for the macrophytes and the lowest δ15N value was found in sediments. Stable carbon and nitrogen isotopes were used to determine the contribution of different food items to the diets of crabs. The δ13C results indicated that the Pseudorasbora parva made the greatest contribution to the diet of Eriocheir sinensis (Chinese mitten crab), while the δ15N results indicated that most food items contributed more than 10% to the diet of the crab. There were three trophic levels identified in the system (Levels 0–2). The crab Eriocheir sinensis, fish Pseudorasbora parva and Misgurnus anguillicaudatus (Oriental weatherfish), and the oligochaete Limnodrilus hoffmeisteri (Limnodrilus worm), were at the second level, zooplankton were at the first level and suspended particulate matter and macrophytes were at trophic position 0.