Farmland shelterbelt system (FSS) in oasis desert ecotones can effectively improve ecosystem services, especially in fragile agricultural areas. However, the spatial-temporal heterogeneity of its ecological effects still needs further clarity, because the interactions are complex and multiple. Understanding this allows us to know the key practical significance of ecological construction and agricultural management. In this study, four typical patterns of FSS (i.e. two lines pattern, TWLP; four lines pattern, FOLP; five lines pattern, FILP; eight lines pattern, EILP) were selected in a desert oasis ecotone in northern China to assess the distributions at vertical (0–100 cm), horizontal (0–3 H) and temporal (May- October) scales of soil properties, vegetation attributes, microclimates and variations of soil moisture storage (SMS) and soil salt contents (C) during the three growing seasons. The results showed that the major difference in soil properties and vegetation attributes of FSSs are the soil particle composition and canopy size, respectively. In FOLP and EILP, the silt contents were 51.6% and 41.5% respectively. The canopy size ranked from the highest to lowest values as follows: FOLP (8.70 m²) > EILP (6.91 m²) > TWLP (4.64 m²) > FILP (4.47 m²). Compared to the control, all patterns of FSSs registered significant effects on microclimate improvement. The FOLP and FILP achieved the same effects as well as EILP, with less spatial costs. Moreover, the variations of SMS and C were mainly different at the vertical scale. As indicated by the Redundancy (RDA) and variation partitioning (VP) analyses, soil properties played a more important role in reserving soil water and controlling soil salinity than vegetation attributes and microclimates, which the independent influence can explain 48.5% of total influence among all factors. Our results provide an efficient theoretical basis for FSS construction and agricultural water management practices.