Myxomatous mitral valve disease (MMVD) is the most common heart disease in small-breed dogs, often leading to heart failure. Oxidative stress in MMVD can harm mitochondria, decreasing their DNA content. This study assesses dogs’ oxidative stress and mitochondrial DNA at different MMVD stages. Fifty-five small-breed dogs were categorized into four groups, including: A—healthy (n = 15); B—subclinical (n = 15); C—heart failure (n = 15); and D—end-stage MMVD (n = 10). Serum malondialdehyde (MDA) and mitochondrial DNA in peripheral blood were analyzed. Quantitative real-time PCR measured mitochondrial DNA, and PCR data were analyzed via the fold-change Ct method. Serum MDA levels were assessed using competitive high-performance liquid chromatography (HPLC). Mitochondrial DNA was significantly lower in group B (−0.89 ± 2.82) than in group A (1.50 ± 2.01), but significantly higher in groups C (2.02 ± 1.44) and D (2.77 ± 1.76) than B. MDA levels were notably elevated in groups B (19.07 ± 11.87 µg/mL), C (23.41 ± 12.87 μg/mL), and D (19.72 ± 16.81 μg/mL) in comparison to group A (9.37 ± 4.67 μg/mL). Nevertheless, this observed difference did not reach statistical significance. It is noteworthy that mitochondrial DNA content experiences a decline during the subclinical stage but undergoes an increase in cases of heart failure. Concurrently, oxidative stress exhibits an upward trend in dogs with MMVD. These findings collectively suggest a potential association between mitochondrial DNA, oxidative stress, and the progression of MMVD in small-breed dogs.