The invention relates to the field of plant genetic engineering, and in particular relates to separation, cloning and application of a gene OsPTR9 which can improve nitrogen utilization efficiency and yield of rice. The OsPTR9 is one gene in a rice PTR (peptide transporter family) family, and an encoded protein is a nitrogenous organic matter transporter. In the invention, the OsPTR9 gene is excessively expressed, so that nitrogen fertilizer absorbing efficiency of normal rice is improved, tillering capacity is improved, ear length and thousand seed weight are increased, and functions of the OsPTR9 gene is verified in an OsPTR9 target gene mutant by adopting an RNAi (ribonucleic acid interference) technology. According to the invention, the expression quantity of the OsPTR9 gene is increased or reduced by adopting a genetic engineering technology, which sufficiently shows that the OsPTR9 gene can control the nitrogen absorption, plant tillering, ear length and thousand seed weight andthe like of the rice. The gene has important application values in the aspects of explaining influence of nitrogen on a plant growth and development process, efficiently utilizing nitrogen fertilizerfor the rice and improving the yield.