The invention provides an intensive treatment method and system for complex high-concentration organic ammonia-nitrogen wastewater. The system includes a water collecting regulating tank, an oil separator, a coagulation reaction tank, a inclined tube sedimentation tank, a Fenton reaction tank, an air flotation device, a Biochemical regulation tank, an A/O biochemical pool, an MBR membrane tank, anultrafiltration system, a same-position nitrification denitrification filter bed, a reverse osmosis system and a discharge tank which are connected in sequence; the method comprises the following steps: pre-treating the complex high-concentration organic ammonia nitrogen wastewater, adjusting the pH to acidity, performing flocculation, Fenton oxidation, biochemical regulation, A/O process, membrane treatment, filter bed treatment, reverse osmosis treatment, and up-to standard discharge. The method and the system greatly shorten the residence time of the complex high-concentration organic ammonia nitrogen wastewater in the biochemical treatment process, solve the problem of difficult wastewater treatment, have low maintenance and operation cost, have small floor space, improve operation efficiency, reduce filtration bed treatment and membrane treatment load, and can prolong the service life of the filter bed and membrane and reduce the cost.