Landscape pattern is one of the main influence factors of agricultural non-point sources (NPS) pollution. The study of the relation of landscape and NPS is scarce and steadily become one of the key research areas now. Aimed at the agricultural NPS pollution problem, a study is carried out in the nine typical districts of the upper reaches of the Yangtze River using the location-weighted landscape contrast index(LCI) which is a landscape pattern evaluation method constructed on the base of the source and sink ecological processes theory. The result showed that LCI responded to NPS pollution load significantly, so LCI can be a good indicator in the evaluation of NPS pollution. Then the spatio-temporal characteristics of the LCIs are analyzed, and the reasons of these characteristics are explored. The slope degree, relative distance to the pollution outlets, elevation and the percentages of different land-use patterns are considered as the main reasons of these characteristics. So a new thinking of controlling NPS pollution is provided, that is, controlling the future spatial risk of NPS pollution by planning and managing the landscape spatial pattern. Finally the countermeasures for the control and management of the NPS spatial risk in the upper reaches of the Yangtze River are discussed: (1）strengthen the management and the improvement tillage of the hillside field; (2）strengthen the management of the agricultural spatial landscape pattern, minimize the NPS pollution load in the outlets form the “source” and “sink” point of view; (3）strengthen the construction of the demonstration areas which control the agricultural NPS pollution spatial risk to perfect the theory and the practice of controlling NPS pollution from the landscape pattern point of view.