The mouse is an important animal model for hearing science. However, our knowledge of the relationship between mouse middle-ear (ME) anatomy and function is limited. The ME not only transmits sound to the cochlea in the forward direction, it also transmits otoacoustic emissions generated in the cochlea to the ear canal (EC) in the reverse direction. Due to experimental limitations, a complete characterization of the mouse ME has not been possible. A fully coupled finite-element model of the mouse EC, ME, and cochlea was developed and calibrated against experimental measurements. Impedances of the EC, ME, and cochlea were calculated, alongside pressure transfer functions for the forward, reverse, and round-trip directions. The effects on sound transmission of anatomical changes such as removing the ME cavity, pars flaccida, and mallear orbicular apophysis were also calculated. Surprisingly, below 10 kHz, the ME cavity, eardrum, and stapes annular ligament were found to significantly affect the cochlear input impedance, which is a result of acoustic coupling through the round window. The orbicular apophysis increases the delay of the transmission line formed by the flexible malleus, incus, and stapes, and improves the forward sound-transmission characteristics in the frequency region of 7-30 kHz.