The Majiayao culture (5300 ~4000cal. aB. P.) is the mainstream culture of the Neolithic period in Gansu- Qinghai region. Studies on the spatial-temporal variation and transition of subsistence strategy have made substantial progress, but the topographic and hydrologic environment of its different phases remains unclear. Based on the concept of site catchment" and aided by GIS methods, this work analyzes surrounding flat lands and corresponding flow accumulation of different phases of Majiayao culture. The study area(33°24'~39036'N,98°42'~106°42'E), covering the western Loess Plateau and north-eastern Tibet Plateau and stretches about 380km from west to east, is the core distributional region of Majiayao culture. The published atlas of Chinese relics, which summarizes former national archaeological survey results, and SRTM data with 90meters resolution are used as the data source of our analysis. Giving consideration to the affection of topographic fluctuation, the site catchment of each cultural phase is defined by cost distance analysis of Arc GIS. Within the site catchment of each Majiayao cultural phase, the flat lands levels and corresponding sum flow accumulation are counted to evaluate the available farm lands and accessible irrigation ground water for agricultural activity. Hydrologic and topographic modules of ArcGIS are used to generate the two indexes and zonal statistics tool is used to indicate the comparable results. Our results indicate that the availability of flat lands and flow accumulation within the site catchment reflects the ancient land use pattern of different phases of Majiayao culture. That is, the proportion of high level flat lands (13~ 15)of Majiayao and Banshan phase is not remarkably higher than other levels. This indicates the two cultural phases don't particularly emphasize the cultivation of flat lands. The corresponding sum flow accumulation of high level flat lands doesn't keep a high level either indicating an unsatisfactory land-water allocation for agricultural activity. The land-water allocation of Banshan is even worse comparing to Majiayao phase. The Machang phase manifests a different situation with high proportion of high level flat lands within its site catchment. Its sum flow accumulation remains a distinguished for all the high level flat lands(13 ~ 15). This indicates a good land-water allocation for massive agricultural activity. We believe that the land use pattern indicated by the flat land level and sum flow accumulation relates to ancient subsistence strategy to a great extent. This work provides new perspective to understand ancient people's selection on living space and subsistence strategy in the context of variable climate condition.