It is effective to evaluate magnetic resonance (MR) images for diagnosing neonatal cerebral disorders because they often accompany the deformation of the brain shape. However, there are many difficulties when radiologists manually extract cerebral surface from the MR images. Therefore, it requires to extract the cerebral surface from neonatal MR images automatically. There are many methods to extract cerebral surface from adult MR images, but there are few methods for neonatal MR images. This paper proposes a new extraction method based on particle method. The proposed method introduces three kinds of particles corresponding to cerebrospinal fluid, gray matter and white matter. First, particles are assigned according to the cerebral shape. Second, particles are moved to form the homogeneous particles, and are transited to the other particles with respect to MR signal. The proposed method was applied to neonatal MR images. The results showed that the proposed method extracted cerebral surface with high accuracy.