The dandelion-shaped nanostructure of an organotin complex with formula Sn(CH3)2Cl2}NC5H4C(O)NHP(O)[NHC6H11]2}2 (C1) was synthesized by means of a sonochemical method. Nano-structures were characterized by elemental analysis, NMR, SEM-EDS, XRD, UV–Vis, and FT-IR spectroscopy. The thermal stability of the complex C1 has been studied by thermal gravimetric analysis (TGA), and compared to the bulk form (C2). Both the morphology and the size of the ultrasound-assisted synthesized organotin complex have been investigated using scanning electron microscopy (SEM) by changing such parameters as the concentration of initial reactants and the sonication frequency. Two different forms of the organotin complex (C1, C2) and the corresponding ligand (L) were evaluated by a modified Ellman’s method on acetyl- and butyrylcholinesterase enzymes. Nanodendalion C1 and ligand L showed the best activity against AChE and BChE, respectively, with the IC50 values being 326.59 μg/ml and 426.68 μg/ml. Further, Lineweaver Burk plots indicated that these compounds are mixed inhibitors. The synthesized compounds and cholinesterase enzymes were simulated by molecular docking for more details concerning the conformation and the orientations of these compounds in the active site of the receptor.