Cholangiocarcinoma is a highly malignant tumor. It is not sensitive to radiotherapy and chemotherapy and has a poor prognosis. At present, there is no effective treatment. As a new method for treating cancer, magnetic fluid hyperthermia has been clinically applied to a variety of cancers in recent years. This article introduces it to the cholangiocarcinoma model and systematically studies the effect of magnetic fluid hyperthermia on cholangiocarcinoma. Starting from the theory of magnetic fluid heating, the electromagnetic and heat transfer models were constructed in the finite element simulation software COMSOL using the Pennes biological heat transfer equation. The Helmholtz coil was used as an alternating magnetic field generating device. The relationship between the magnetic fluid-related properties and the heating power was analyzed according to Rosensweig’s theory. After the multiphysics coupling simulation was performed, the electromagnetic field and thermal field distribution in the hyperthermia region were obtained. The results showed that the magnetic field distribution in the treatment area was uniform, and the thermal field distribution met the requirements of hyperthermia. After the magnetic fluid injection, the cholangiocarcinoma tissue warmed up rapidly, and the temperature of tumor tissues could reach above 42 °C, but the surrounding healthy tissues did not heat up significantly. At the same time, it was verified that the large blood vessels around the bile duct, the overflow of the magnetic fluid, and the eddy current heat had little effect on thermotherapy. The results of this article can provide a reference for the clinical application of magnetic fluid hyperthermia for cholangiocarcinoma.