The structural, mechanical, thermodynamic and electronic properties of indium (In) substitution for W and Se as well as intercalating In in bulk WSe2 have been investigated by first-principles calculation. The dopant indium is more likely to substitute for W (or Se) under Se-rich (or W rich) conditions. Doping decreases the elastic modulus, hardness, Debye temperature and the minimum thermal conductivity of WSe2 (e.g., InW8Se16 has the lowest values) but effectively improves the ductile and lubrication property (e.g., InW7Se16 and InW8Se16 present a largest ductile and lubrication property, respectively). WSe2 together with the dopant are all anisotropic. InW8Se16 performs the largest degree of anisotropy among them. Indium doping cannot introduce magnetism. However, it can transform the semiconductor of pure WSe2 to semimetal. Both of the substituted structures character the p-type doping nature while the intercalated structure characters the n-type doping nature. The hybridization of W-d and Se-p electrons are the main cause of the W–Se covalent bond. New covalent bonds are formed for the In-doped structures.