Pulmonary hypertension syndrome (PHS) is a poultry disease that causes significant economic losses in broilers. Portal hypertension and liver cirrhosis can cause ascites formation. Disturbance of mitochondrial dynamics causes several diseases; however, its mechanism of action in PHS is not yet fully understood. In this research, 210 broilers were split randomly into two groups: control and PHS. Broilers in the control group were injected with normal saline and those in the PHS group were injected with CM-32 cellulose particles at 20 days of age. Transmission electron microscopy (TEM) was used to assess mitochondrial ultrastructure. Changes in mitochondrial dynamics were measured by immunohistochemical staining, RT-PCR and western blotting. On days 28 and 42, the liver and heart were collected from each group, and the ascites heart index (AHI) and hepatic coefficient were calculated. The results showed that PHS induced hepatocyte damage, reduced mitochondrial size, and increased mitochondrial number. Furthermore, RT-PCR demonstrated the downregulation of Mfn1, Mfn2, and Opa1 mRNA, and the upregulation of Drp1 and Mff mRNA. Protein expression levels detected by immunohistochemistry and western blotting were similar to those obtained by RT-PCR. This study showed that mitochondrial fusion in the liver was diminished and mitochondrial fission in the liver was enhanced in PHS broilers.