The Loess Plateau is one of the most erodible areas in the world, and numerous conservation measures have been implemented to control severe soil erosion. Better understanding of the changes in runoff and their influencing factors is required. A vector autoregression (VAR) model was used to simulate the dynamic relationship between runoff and six factors (precipitation, terraces, afforestation, grassing, check dams' construction, and grazing fencing) based on precipitation, runoff, and controlling measures of the Tuwei River basin in the middle reaches of the Yellow River during 1959–2012. Results showed that response of runoff usually lagged behind precipitation and the implementation of soil and water conservation measures. The annual runoff has no response to the increase of each measure area at the first year, but has varying degrees of response from the second year onward. Moreover, the same measure has different effects on runoff in different periods. The contribution of the factors that affect the annual runoff varied in the order of grazing fencing hillside < grassing < check dams' construction field < afforestation < precipitation < terraces. In the long term, the contribution of soil and water conservation measures would be greater than 70% in the fluctuation of annual runoff.