Thyroid hormone is an important factor for proper development of the mammalian brain. Perinatal hypothyroidism leads to long-term behavior and neuromotor competence alterations in humans and animals. Our study aimed to investigate the effects of perinatal hypothyroidism on behavior changes of rat pups and its relation with the apoptosis of hippocampus neurons. Behavior tests were taken to evaluate the effects caused by perinatal hypothyroidism. TUNEL staining was used to analyze the apoptosis of neurons on CA3 region of hippocampus. The study suggested that perinatal hypothyroidism affects behavior development, as well as leading to the decrease in spatial learning and memory capability. This condition can be improved with hormone substitute treatment. Furthermore, the changes of learning and memory capability are closely related to the increasing number of apoptotic neurons in the hippocampus.