In the present work, the crystal structure and microstructure of martensite in Ni-Mn-In alloys and the variant rearrangement behavior under the external mechanical loading were investigated. Results show that the martensite has an incommensurate 6M modulated structure (I2/m (α0γ)00) with the modulation wave vector q = 0.3437c*. Microstructure of martensite is in plate shape and self-organized with four orientation variants that are alternately distributed and related in either type-I, or type-II or compound twin relation. The variant interfaces are in coincidence with their corresponding twinning plane and then should be considered coherent. Under the uniaxial compression, the loading located in the common positive Schmid factor zone of the three types of detwinning systems might be favorable to obtain the single variant state. This study is expected to offer a fundamental information of crystal structure, microstructures and variant rearrangement behaviors in Ni-Mn-In alloys, so as to understand the underlying mechanisms of their multifunctional magneto-responsive properties.