The invention provides a brain disease detection system based on brain pathological age estimation. The brain disease detection system comprises image acquisition equipment, actual age input equipment, a storer, a preprocessing module, a feature extraction module, a feature selection module, a brain pathological age estimation module, a parameter optimization module, a classified recognition module and a result output module; the storer is provided with a VCI sample database, a CTL sample database and a database to be measured. The brain disease detection system has the advantages that the system fully utilizes brain magnetic resonance image characteristics, in combination with the actual age information of samples, simulation training is conducted through a great number of samples, and the obtained brain pathological age estimation module can effectively estimate the brain pathological age of a measured object; meanwhile, deviation between the brain pathological age estimation value and the actual age serves as supplementary information, whether a patient suffers from brain disease or not is effectively diagnosed through infusion with brain image information, the whole system is definite in principle, convenient to implement, more scientific basis is achieved for brain disease detection, reliability is high, and feasibility is high.