Phosphorus (P) is the major controlling factor for the eutrophication in the water. After the external P pollution is gradually controlled, the influence of surface sediments as the main source of endogenous phosphorus on the water quality of the Yellow River can not be ignored. It is of great significance to master the accumulated degree of various P fractions in surface sediments and exchange ability of phosphorus at the water-sediment interface for administering the water environment and regulating the P load. In this study, surface sediments of high-water period (2011. 07), low-water period (2014. 05) and normal-water period (2014. 10) from Gansu, Ningxia and Inner Mongolia sections of the Yellow River were collected, respectively. The contents of various phosphorus fractions were determined by using standards measurements and testing (SMT) method and molybdenum antimony spectrophotometry, and the isothermal adsorption and adsorption kinetics processes of P in surface sediments were simulated in the laboratory. This study found: (1) compared with the characteristics of phosphorus fractions of surface sediments in major rivers of China, the content of OP was as low as that of NaOH-P, and the content of HCl-P was higher in surface sediments. The average phosphorus content of all fractions was the highest at high-water period, indicating that the accumulated degree of phosphorus in surface sediments was the highest at high-water period and the water environment of the study area was greatly impacted by the development of agriculture along the route. So, reasonable use of phosphorus fertilizers and optimizing irrigation return water quality will be the developing direction to reduce the risk of phosphorus pollution in the Yellow River in the future. (2) comparing the equilibrium phosphorus concentration (EPC0) of surface sediments at all sampling sites from isothermal adsorption for low phosphorus concentrations with the criterion about the phosphorus concentration threshold of the eutrophication in the water, we found that surface sediments at most sampling sites played a role as “phosphorus source”, and there was a trend of phosphorus release from sediments to overlying water, especially for most sampling sites with high values of EPC0 in low-water period, the release trend was more obvious. Based on the fitting parameters of L model and F model from isothermal adsorption at high phosphorus concentrations, the retention capacity of surface sediments to phosphorus in high-water period was the strongest, followed by low-water period and the minimum in normal-water period, the adsorption processes of surface sediments on phosphorus in all sampling sites were easy to occur. Based on the changed trend of kinetics curves of phosphorus adsorption, we found phosphorus adsorbent contents of all selective sampling sites increased rapidly in the first 12 h, increased gradually and tended to be stable during 12 h to 48 h. According to fitting results of the pseudo-second-order kinetics for adsorption kinetics processes, the reaction rate of phosphorus adsorption on surface sediments was mainly controlled by chemisorption. According to results that different sampling sites at the same water period had different rate-limiting steps and the pore diffusion was the rate-limiting step in nearby sampling sites at different water periods, we inferred differences of composition and physicochemical properties of surface sediments on phosphorus adsorption rate had a greater influence than variances of flow rates and flow fluxes of overlying water among different water periods.