[Objective] Minimum ecological flow (e-flow) targets are increasingly used as enforceable constraints in basin management, but their spatiotemporal reliability and ecological representativeness remain insufficiently evaluated at large scales. This study aims to quantify e-flow compliance across the Yangtze River Basin (YRB), identify the drivers of noncompliance and spatial heterogeneity, examine how compliance aligns with river ecological environment conditions, and propose targeted recommendations for improving goal setting, monitoring, and assessment. [Methods] The daily e-flow compliance records were compiled for 114 key control cross-sections from the Yangtze River Water Resources Commission’s monthly monitoring bulletins between January 2023 and July 2024. Compliance was summarized as (i) whether each cross-section met the minimum target throughout the full study period, and (ii) the number of noncompliant days at each cross-section and by month. For ecological environment linkage, 40 e-flow cross-sections were matched with nearby national automated surface-water quality stations, and dissolved oxygen, permanganate index, total nitrogen, total phosphorus, and water-quality class were examined. Subsequently, a four-quadrant diagnostic framework was constructed using mean noncompliance days and the mean share of days classified as Class Ⅳ to Inferior Ⅴ. [Results] Throughout the study period, 71 of 114 cross-sections (62%) fully met the minimum e-flow targets, whereas 43 cross-sections (38%) experienced noncompliance ranging from 1 to 170 days (mean 25.8 d; median 5.0 d). Compliance exhibited a pronounced seasonal unimodal pattern, with lower performance in winter and spring and higher performance in summer and autumn. Specifically, 901 noncompliance days occurred from January to March and from November to December, compared to only 118 days from April to October. Notably, all cross-sections met targets in August. Interannual variability was substantial. From January to July, the number of noncompliance days decreased from 814 in 2023 to 335 in 2024, and the monthly average number of noncompliant cross-sections declined from 18.8 to 10.5. Spatially, heterogeneity was strong among secondary basins, and the left bank outperformed the right bank. Mechanistically, major contributors included seasonal unevenness in precipitation and runoff, differences in dam regulation, reduced mainstream-to-lake diversion affecting the Dongting system, intensive agricultural withdrawals in lake-dominated right-bank regions, and governance and measurement challenges in cross-province water allocation. For the 40 paired sites, pollutant indicators showed no significant monotonic relationship with e-flow compliance, and the total phosphorus could even appear lower in low-flow and noncompliant months due to particulate phosphorus dynamics. The quadrant analysis indicated that 60% of sites fell into high-match zones, but 16 sites showed notable mismatches, suggesting that e-flow compliance was a necessary but insufficient condition for good ecological environment status and that relying solely on flow as a warning indicator remained uncertain. [Conclusion] Large-scale e-flow compliance in the YRB is generally favorable but exhibits strong seasonal, interannual, and governance-linked spatial heterogeneity. To improve ecological relevance and management effectiveness, the following recommendations are proposed: (i) shifting from fixed single-value targets to higher time-resolution, multi-objective, and adaptively updated e-flow targets; (ii) optimizing monitoring networks to better cover ecological hotspots (e.g., key spawning habitats), implementing flexible temporal resolution, and conducting emergency monitoring during rapid ecological events; (iii) transitioning from flow-only, section-based assessment toward integrated basin-scale evaluation that couples flow, water quality, habitat, and biodiversity outcomes.