Dam construction causes the accumulation of phosphorus in the sediments of reservoirs and increases the release rate of internal phosphorus (P) loading. This study investigated the longitudinal variability of phosphorus fractions in sediments and the relationship between the contents of phosphorus fractions and its influencing factors of the Manwan Reservoir, Lancang River, Yunnan Province, China. Five sedimentary phosphorus fractions were quantified separately: loosely bound P (ex-P); reductant soluble P (BD-P); metal oxide-bound P (NaOH-P); calcium-bound P (HCl-P), and residual-P. The results showed that the total phosphorus contents ranged from 623 to 899 µg/g and were correlated positively with iron content in the sediments of the reservoir. The rank order of P fractions in sediments of the mainstream was HCl-P>NaOH-P>residual-P>BD-P>ex-P, while it was residual-P>HCl-P>NaOH-P>BD-P>ex-P in those of the tributaries. The contents of bio-available phosphorus in the tributaries, including ex-P, BD-P and NaOH-P, were significantly lower than those in the mainstream. The contents of ex-P, BD-P, NaOH-P showed a similar increasing trend from the tail to the head of the Manwan Reservoir, which contributed to the relatively higher content of bio-available phosphorus, and represents a high bio-available phosphorus releasing risk within a distance of 10 km from Manwan Dam. Correlation and redundancy analyses showed that distance to Manwan Dam and the silt/clay fraction of sediments were related closely to the spatial variation of bio-available phosphorus.