The objective of this study was to identify functional genes regulating root branching and drought resistance that could be used in developing drought-tolerant alfalfa (Medicago sativa L.) cultivars. Heterologously expression of an Arabidopsis orphan gene QQS was found to enhance root branching and drought tolerance in alfalfa. By yeast two-hybid (Y2H) and luciferase complementation imaging (LCI) assay, a transcription factor MsNF-YC4 was confirmed as an endogenous interactor of QQS. We speculated it could play a positive role in regulating alfalfa root branching and drought tolerance. Transgenic alfalfa plants overexpressing MsNF-YC4 were generated by Agrobacterium-mediated transformation. Through RNA sequencing (RNA-seq), we noticed that the abscisic acid and auxin signaling pathways were affected in the MsNF-YC4 overexpressing plants. Consistently, exogenous application of indoleacetic acid also enhanced root branching and drought tolerance of alfalfa seedlings. Further, MsNF-YC4 was found to activate the transcription of MsARF8 by yeast one-hybrid (Y1H) and dual-luciferase (LUC) reporter Assay. Silencing of MsARF8 by antisense oligonucleotide (as-ODN) method suppressed both root branching and drought tolerance of alfalfa seedlings. Collectively, we prove that an endogenous transcription factor MsNF-YC4 interacts with foreign protein QQS, and by activating MsARF8 to regulate alfalfa root branching and drought resilience. Our study also provides a regulatory pathway for drought tolerant alfalfa breeding.