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Phosphorus (P), a non-renewable essential resource, faces heavy exploitation and contributes to eutrophication in aquatic environments. Assessing P input is vital for a healthier P cycle in the Upper Yangtze River (UYR), a phosphate ore rich basin, where P mining and P chemical enterprises have prominent pollution problems. This study modified the net anthropogenic phosphorus input (NAPI) model to include ore mining P input (P ore). We analyzed the evolutionary characteristics of P input in five sub-basins of UYR from 1989 to 2019 using prefecture-level data, and assessed the uncertainty of the data. NAPI in all sub-basins exhibited an upward and then downward trend during 1989–2019, with the inflection point occurring in 2015 or 2016, showing a net increase of about 1.1 times (568–1162 kg P km−2 yr−1) in the whole UYR basin. Among the components of NAPI, P fertilizer inputs (P fer) and food/non-food and feed P inputs (P f/nf&feed) contributed comparably, though the growth rate of P fer was most notable basin-wide. P ore proportion increased significantly (about 3-fold), with a peak of 20%, especially in Wujiang sub-basin. The multi-year (1989–2019) average NAPI in UYR rose sequentially from west to east, with hotspot areas mainly concentrated in the Sichuan-Chongqing urban agglomeration and cities of Hubei province. The regional P input closely related to the population density and the level of agricultural development, certainly the phosphate mining was also unignorable. This study emphasizes that based on current status of NAPI development in UYR, targeted management for different regions should focus on improving agricultural P use efficiency and rational exploitation of P mineral resources. [Display omitted] • Optimization of the NAPI model complements P inputs from mining and beneficiation. • The contribution of P ore inputs an overall increasing trend, especially in Wujiang. • Degree of population concentration was a key driver for NAPI. [ABSTRACT FROM AUTHOR]