Pulmonary fibrosis (PF) is a progressive, fatal lung disease lacking effective treatments. Autotaxin (ATX) plays a crucial role in exacerbating inflammation and fibrosis, making it a promising target for fibrosis therapies. Herein, starting from PAT-409 (Cudetaxestat), a series of novel ATX inhibitors bearing 1H-indole-3-carboxamide, 4,5,6,7-tetrahydro-7H-pyrazolo[3,4-c]pyridin-7-one, or 4,5,6,7-tetrahydro-1H-pyrazolo[4,3-c]pyridine cores were designed based on the structure of ATX hydrophobic tunnel. The optimal 31 and 35 inhibited ATX with IC50 values of 2.8 and 0.7 nM, respectively. In a bleomycin-induced mouse PF model, both compounds significantly reduced fibrosis by regulating the TGF-β/Smad signaling pathway and downregulating collagen deposition. Furthermore, 35 exhibited both negligibly low hERG channel inhibition (IC50 > 30 μM) and remarkable microsomal stability. Notably, 35 was characterized by favorable pharmacokinetic properties (F = 69.5%) and excellent safety in vivo. Overall, 35 turned out to be a well-characterized potent and safe ATX inhibitor warranting further investigation for the treatment of PF.