In the present work, the crystal structure, microstructure and martensitic transformation path in Ni-Mn-In alloys were systematically studied. Results show that the austenite has a highly ordered cubic L21 structure. The martensite phase possesses a 6M incommensurate monoclinic modulated structure. The microstructure of martensite is in plate shape and self-organized in colonies. The maximum of 6 distinct martensite colonies and 24 kinds of variants in one parent grain are observed. Both of K-S and Pitsch orientation relations are found to be appropriate to describe the lattice correspondence between the parent and product phase. However, the transformation path related to Pitsch relation should be the real one that governs the transformation process in Ni-Mn-In alloys. With the determined martensitic transformation path, the formation mechanism of the microstructure of martensite phase is revealed. The 6 distinct martensite colonies are respectively generated by the six (110) planes of the cubic austenite phase during martensitic transformation. Each (110) plane transforms into four twin-related variants by changing the directions of the transformation plane and direction.