Hydrogen sulfide (H2S), the third gasotransmitter, plays important roles in cancer biological processes. As endogenous H2S exerts pro-cancer functions, inhibition of its production in cancer cells may provide a new cancer treatment strategy and be achieved via regulation of the function of cystathionine beta-synthase (CBS), one of the main metabolic enzymes synthesizing H2S. This enzyme plays important roles in the development and progression of colon and ovarian cancer, primarily regulating mitochondrial bioenergetics and accelerating cell cycle progression. In the present study, we firstly investigated the role of the CBS/H2S system in human hepatoma cells, and then the inhibitory effect of a quinolone-indolone conjugate QIC2 on this system. When CBS was overexpressed in human hepatoma HepG2 and SMMC-7721 cells, inhibition of endogenous CBS/H2S significantly reduced their viability and growth rate, as well as the proliferation of SMMC-7721 cells. Meanwhile, CBS knockdown caused multiple effects, including apoptosis of SMMC-7721 cells, an increase in the Bcl-2-associated X protein (Bax)/B cell lymphoma/leukemia (Bcl-2) ratio, activation of caspase-3 and polyADP-ribose polymerase (PARP), when compared with the scramble siRNA (Sc siRNA)-transfected groups. Heme oxygenase-1 (HO-1; a microsomal enzyme) expression was significantly decreased while the reactive oxygen species (ROS) level was increased in the CBS siRNA-transfected SMMC-7721 cells. QIC2 significantly reduced SMMC-7721 cell viability in a dose-dependent manner and showed a lower toxicity in human normal liver HL-7702 cells relative to the positive controls sunitinib and doxorubicin (DOX). The compound also inhibited cell proliferation and induced cell apoptosis in SMMC-7721 cells. Further analysis indicated that QIC2 downregulated the CBS/H2S system, decreased both HO-1 protein and glutathione (GSH) levels while increased the ROS level and activated the caspase-3 cascade. Collectively, our results demonstrated that the CBS/H2S system plays important roles in human hepatoma cells and QIC2 significantly inhibited cell growth via downregulation of the system.