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With rapid socioeconomic development, extra demands have been placed on the waterway sustainable exploration, which are closely related to river ecological protection, flood control and comprehensive utilization of water resources. Therefore, it is theoretically and practically relevant to investigate the waterway carrying capacity (WCC) under multi-objective coordination. Based on a hierarchical indicators system framework of WCC which including four subsystems (i.e., economic-demand system, flood-control system, water-supply system and ecological-protection system), we propose a fuzzy comprehensive evaluation model of WCC, which covers a flow module, a sediment module, an ecological module and a comprehensive analysis module. This model integrates two assessment methods of comprehensive index evaluation and fuzzy-pattern recognition with analytic hierarchy process (AHP). Determining weights by the AHP method can avoid the subjectivity and errors caused by weighing a large number of indicators, while the combined two methods have a complementarity of function to more objectively reflect the carrying capacity level of different layers. The WCC of the lower Yangtze River from Hukou to Nanjing reaches was assessed, and the results suggested that the carrying capacity states of waterway are generally on a downward trajectory with the increase of waterway scale, and the carrying capacity levels of waterway for the built (in 2015) and planning scales (in 2030) are in the state of bearable or critical bearable. In a certain future period, the exploitable thresholds of channel scales in the sections from Hukou-Anqing, Anqing-Wuhu and Wuhu-Nanjing reaches are estimated to be 8.0 × 200 × 1050 m, 8.0 × 200 × 1050 m and 10.5 × 500 × 1050 m, respectively. The evaluation results are generally consistent with exiting studies, thus the proposed model is effective to identify the threshold of waterway exploitation under the restriction of multiple factors. This research can provide a reference for the evaluation of WCC in the sustainable development of similar inland waterways.