The effects of site occupation on the phase stability, martensitic transformation, and the magnetic and electronic properties of a full series of Ni-Mn-In alloys are theoretically studied by using the ab initio calculations. Results indicate that the excess atoms of the rich component directly take the sublattices of the deficient components of the Ni2Mn1+xIn1-x, Ni2-xMn1+xIn, and Ni2+xMn1-xIn alloys. Nevertheless, the mixed and indirect site occupations may coexist in the Ni2+xMnIn1-x system. The relevant magnetic configurations of the austenite for the four alloy systems have also been determined. The results show that, except for the austenite in the Ni2-xMn1+xIn alloys, which tend to be ferrimagnetic, the other alloys all present ferromagnetic austenite. Thus, the site occupation and associated magnetic states are the crucial influencing factors of the phase stability, martensitic transformation, and the total magnetic moment. The electronic structure of the austenite phase also shows that the covalent bonding plays an important role in the phase stability. The key finding of this work is both Ni2Mn1+xIn1-x and Ni2+xMnIn1-x alloys serve as the potential shape memory alloys.