This study focuses on the effect of window openings on the seismic performance of the stone walls of Tibetan and Qiang dwellings. A typical stone wall of a Tibetan and Qiang dwelling constructed using irregular stone and yellow mud masonry in Li County, Sichuan Province, was chosen as a prototype, and two stone walls with different structural window openings were designed for proposed static tests and microscopic electron microscope scanning (SEM), which obtained the damage patterns and microscopic damage mechanisms of the walls and analyzed them in comparison with the test results of the stone walls without window openings. At the same time, a finite element model was established based on the test parameters to study the effects of opening size, shape, and aspect ratio on the seismic performance of the stone walls of Tibetan and Qiang dwellings. The findings indicate that “X”-shaped cracks at the corners of the window openings and extending to the surrounding areas are the primary damage characteristics. The unique microstructure of yellow clay and schist leads to the faster appearance of wall cracks. The peak load, stiffness, and energy dissipation of the windowed walls were less than those of the windowless walls. It was found through simulation that the seismic performance of the wall decreases with the increase in the opening size; as the wall’s openings take on different shapes, the ultimate bearing capacity steadily declines with the order of circular, square, triangular, trapezoidal, and rectangular; and under a range of aspect ratios, the wall’s seismic performance is best when the opening’s aspect ratio is 1:1. The research results of this paper are of reference value for the research, design, and construction of stone walls and other non-engineered masonry works of Tibetan and Qiang dwellings.