•This study mainly analyzed changes of root TIPs expression under mycorrhization and drought.•AM plants had higher leaf water status and root ABA levels under WW and DS.•AMF up-regulated PtTIP1;2, PtTIP2;1, PtTIP4;1 and PtTIP5;1 expression under WW.•Root PtTIP1;2, PtTIP 1;3 and PtTIP 4;1 were up-regulated by AMF under DS.•Root PtTIP2;1 and PtTIP 5;1 were down-regulated by AMF under DS. Arbuscular mycorrhizal fungi (AMF) can enhance plant tolerance to drought stress (DS), while it is unclear whether aquaporins take part in the AMF-modulated mechanisms. In this study, a potted experiment was conducted to investigate the effects of an arbuscular mycorrhizal fungus, Funneliformis mosseae, on plant growth, leaf water status, root abscisic acid (ABA), and relative expression levels of root tonoplast intrinsic protein (TIPs, one of the most abundant aquaporins on plant vacuoles and plasma membranes) genes of trifoliate orange (Poncirus trifoliata L. Raf.) seedlings under well-watered (WW) and DS. The 8-week DS significantly decreased mycorrhizal colonization by 19.5%. In both WW and DS, AMF significantly enhanced leaf relative water content, leaf water potential, and plant growth performance (plant height, stem diameter, leaf number, and biomass), as well as root ABA levels. With regards to root TIPs, seven TIP genes were identified. Meanwhile, AMF treatment up-regulated PtTIP1;2, PtTIP2;1, PtTIP4;1, and PtTIP5;1 and down-regulated PtTIP1;1 and PtTIP2;2 under WW. Under DS, AMF seedlings showed higher expression levels of root PtTIP1;2, PtTIP1;3, and PtTIP4;1 and lower expression levels of root PtTIP2;1 and PtTIP5;1. It concludes that root TIPs exhibited diverse responses to mycorrhization, indicating the multiple roles of AMF in water absorption under drought.