Many experiments on LiInSe2 (LISe), a technologically important nonlinear optical crystal, suggest that nonstoichiometric defects play an important role in changing the crystal color and the crystal's optical applications in infrared and/or near-visible regions. The exact defect species and structures remain unverified by either experiment or theory however. Thereby, density functional theory within the (semi)local and hybrid exchange-correlation functional is employed to determine the dominant intrinsic point defects in LISe under various environments. It is found that the isolated point defects In antisite In-Li(2+) and Li vacancy V-Li(-) are dominant in a Li-deficient environment, while the Li interstitial Li-i(+) turns out to be energetically preferable in a Li-sufficient condition. Interstitial In-i(3+) is regarded as an intermediate state to form In-Li(2+) (In-1(3+) + V-Li(-) -> In-Li(2+)) if there is a Li deficiency. In all possible charge-compensated defect complexes as well as Frenkel and Schottky defects, In-Li(2+) + 2V(Li)(-) is the only possible complex configuration under Li-deficient conditions according to the defect structures and formation energies. In particular, the clustering effect decreases the formation energies of all considered defects with respect to the dilute limit. The investigation of the optical response gives further evidence that the intrinsic point defects are responsible for the crystal color change and optical absorption cutoff shift, and conversely, these phenomena could be helpful for recognizing the dominant defects in LISe crystals.