Anion-exchange with high perchlorate affinity resins is one of the most promising technologies for removing low levels of perchlorate. However, the traditional brine desorption technique is difficult and costly for regeneration of this type of resin. Previously, a direct bio-regeneration method by contacting the spent high perchlorate affinity resin with the perchlorate-reducing bacteria was proved feasible. This research is a further study of that method. Firstly, a direct bio-regeneration process model, based on the physicochemical and biological fundamentals, was developed and calibrated with experimental data. Thereafter, the rate-limiting step in regeneration of the high perchlorate affinity resin was investigated. Methods to enhance the regeneration efficiency were developed. The results indicated that the calibrated model well described the regeneration process. It thus might provide useful insights into the regeneration system. The results also demonstrated that the perchlorate desorption from the loaded resin could be the rate-limiting step. Addition of proper amount of counter anions such as chloride and sulfate improved the regeneration efficiency because these anions could promote both the extent and rate of perchlorate desorption from the loaded resin. These findings aided us in achieving good and efficient regeneration of high perchlorate affinity resins like the A-530E and SR-7 resins. The findings also suggested that the application of bacteria that could efficiently reduce perchlorate in highly saline solution would make the method more promising for the regeneration of high perchlorate affinity resins.