A method for predicting the development index of pulsed periodic water flooding in multi-layer reservoir is based on mathematical analysis and optimization theory, synthesizes the static reservoir factor and dynamic development factor, fully refers to and applies coring, secondary interpretation, exist monitoring data, etc. to establish a split calculation method and reasonable injection distribution and injection allocation models. The sub-injection and injection allocation models are respectively formed into software, which can transfer the relevant data from the production database of the research block. The injection allocation quantity of each well and each layer in the block is automatically calculated by the injection allocation model. Through the calculation of separate injection model, the separate injection intervals of water injection wells are automatically given. The invention divides data display, service processing and data storage into different layers. The method maintains the relative independence between the layers, and is especially suitable for the development of large-scale systems. Once the user business rules change, the system has good adaptability, and theworkload of later revision and maintenance is small.