When light propagates through complex medium, such as biological tissue and multimode fiber, refractive index inhomogeneity causes multiple scattering and distortion. This phenomenon is usually seen as obstacles for biomedical imaging, telecommunications, photodynamic therapy and so on. Thus, manipulation of the incident wavefront to compensate for the wavefront distortion due to multiple scattering has been an interdisciplinary subject of interest. Fortunately, wavefront shaping technologies have emerged to provide versatile solutions to minimize the influence of light scattering. By modulating the incident light into a special wavefront with a spatial light modulator, focusing through scattering medium is obtained. To date, several wavefront shaping techniques have been proposed, mainly including transmission matrix inversion, feedback based iterative optimization, and digital optical phase conjugation. Unlike a planar wavefront, the modulated light with special wavefront is transformed into a bright optical focus spot or a desired focus pattern after the scattering medium. Among the proposed approaches, the transmission matrix is considered as a significant tool to characterize a multiple scattering medium with the purpose of manipulating light propagation through it, which contains all the information related to the input field and the scattered output field. In this work, we experimentally measure the transmission matrix of scattering media based on self-reference interference method with a digital micromirror device. Unlike the conventional setup, which divides the incident wavefront into a signal part and reference part, in the self-reference interference method, the reference light is superimposed directly on the signal light to form a new set of input light fields. This self-reference interference method effectively improves the degree of freedom of optical field modulation. Moreover, the intensity ratio between the signal light and the reference light can be adjusted conveniently. In our experiment, this superimposed field is generated by a digital micromirror device with superpixel method. We measure the Hadamard basis and the OAM-basis transmission matrices of scattering medium, respectively. With the measured transmission matrices, single-spot, multi-spot and vortex focusing are achieved after scattering medium, verifying the accuracy of the measured transmission matrices. The strong diagonal presented in the norm of focusing operator also proves the accuracy of the measured transmission matrices. The proposed method may have potential applications in optical imaging and optical communication under scattering environment.