A novel process coupling photosynthetic bacteria (PSB) with electrodeionization (EDI) treatment was proposed to treat high ammonia wastewater and recover bio-resources and nitrogen. The first stage (PSB treatment) was used to degrade organic pollutants and accumulate biomass, while the second stage (EDI) was for nitrogen removal and recovery. The first stage was the focus in this study. The results showed that using PSB to transform organic pollutants in wastewater into biomass was practical. PSB could acclimatize to wastewater with a chemical oxygen demand (COD) of 2,300 mg/L and an ammonia nitrogen (NH4+-N) concentration of 288–4,600 mg/L. The suitable pH was 6.0–9.0, the average COD removal reached 80%, and the biomass increased by an average of 9.16 times. The wastewater COD removal was independent of the NH4+-N concentration. Moreover, the PSB functioned effectively when the inoculum size was only 10 mg/L. The PSB-treated wastewater was then further handled in an EDI system. More than 90% of the NH4+-N was removed from the wastewater and condensed in the concentrate, which could be used to produce nitrogen fertilizer. In the whole system, the average NH4+-N removal was 94%, and the average NH4+-N condensing ratio was 10.0.