Traf2 and Nck-interacting kinase (TNIK) is the downstream molecule of Wnt/β-catenin signal pathway. As the activation kinase of β-catenin/T-cell factor 4 transcription complex, it can fully activate Wnt signalling and promote the growth and invasion of tumor cells. We conducted computer-assisted virtual screening and a series of analyses to find potential inhibitors of TNIK. First, LibDock was used for molecular docking of natural small molecules. Then, ADME (Adsorption, Distribution, Metabolism and Excretion) analysis and toxicity prediction were performed on the top 80 small molecules which have higher scores. Additionally, in order to further determine the affinity and binding mechanism of TNIK-ligands, we analyzed the pharmacophores and used CDOCKER for more accurate molecular docking. Last but not least, molecular, dynamics simulation was used to evaluate the stability of receptor-ligand complexes in natural environment. The results showed that natural small molecules (ZINC000040976869 and ZINC000008214460) had high affinity and low interaction energy with TNIK. They were predicted to have excellent pharmacological properties, such as high plasma protein binding capacity and water solubility, no hepatotoxicity, no blood-brain barrier permeability and tolerant with cytochrome P450 2D6 (CYP2D6). In addition, they have less rodent carcinogenicity, AMES mutagenicity, and developmental toxicity potential. Molecular dynamics simulations showed that the two compounds could achieve the stability of potential energy and Root-Mean-Square Deviation (RMSD) at different time nodes. This study proves that ZINC000040976869 and ZINC000008214460 are ideal lead compounds with inhibition targeting to TNIK. These compounds provide valuable ideas and information for the development of new colorectal cancer targeting drugs.