Asymmetric cell division is a critical aspect of many stem cells in balancing self-renewal and differentiation. For those stem cells residing in the niche, spindle orientation with respect to the niche is crucial to achieve asymmetric stem cell division. Despite this critical relationship between the stem cell niche and spindle orientation, the niches’ role in spindle orientation is poorly understood. Here we show that, in Drosophila male germline stem cell (GSC) niche, niche ligand Upd and its receptor Dome, but not their downstream JAK-STAT pathway, is required for spindle orientation. We found that the receptor Dome directly interacts with a plus-end microtubule binding protein Eb1 to orient the spindle toward the niche. Live imaging experiments suggest that Dome and Eb1 function to pull the spindle toward the niche. Photoconversion experiments demonstrate that microtubule dynamics is asymmetric between apical and basal half of the spindle, possibly explaining the mechanism by which spindle is pulled toward the niche. Our study reveals a novel mechanism by which the niche directly governs the asymmetric stem cell division via direct regulation of microtubule cytoskeleton.