The invention discloses an advanced treatment process and system for micro-polluted source water. The process comprises the following steps: 1, conducting oxidation pretreatment on micro-polluted raw water through ozone to obtain the oxidized raw water; 2, primarily filtering the oxidized raw water, and removing suspended solids through physical adsorption to obtain primarily filtered raw water; 3, physically adsorbing the primarily filtered raw water through a sand layer and carrying out biologically degrading through a microbial film to obtain drinking raw water; 4, filtering the drinking raw water through activated carbon, carrying out disinfection by ultraviolet light to complete the advanced treatment of the micro-polluted source water, and conveying the finally obtained water to a user to use. The system comprises a raw water supply device, an ozone pretreatment device, a rough filtering treatment device, a micro-biological degradation device, an activated carbon filtering device and a collected water disinfection device. The process integrates ozone oxidization, physical adsorption, micro-biological degradation, and activated carbon physical-chemical adsorption into a whole. The overall process is reasonable in method, and simple to operate, the structural design is ingenious, and the process and the system are safe and efficient.