In this paper, a three-segmented counterflow (COUN) electrodialysis (ED) for ammonia (NH4+-N) and potassium (K+) treatment in liquid anaerobic digestate (LAD) was proposed to break the high-concentration limit of nutrient recovery without sacrificing the ion removal performance and energy efficiency. The effects of the COUN operation mode on ED performance were studied based on pilot-scale experiments. The results indicate that the COUN mode improves the distribution of concentration difference (Δc). Hence, the ion fluxes of NH4+-N and K+ have increased by 51.0% and 25.3%, respectively. A highly concentrated product (NH4+-N at 10428 ± 225 mg/L and K+ at 7500 ± 156 mg/L) can be obtained, and the concentration multiples of NH4+-N and K+ have increased by 14.1% and 9.8%, respectively, with slight effects on their removal rates. The current efficiency for NH4+-N and K+ was increased by 38.1% and 14.5%, reaching 54.7 ± 3.5% and 12.4 ± 0.5%, respectively, and the final energy consumption of 3.8 ± 0.2 kWh/kg-N) has reduced by 31.8%. The non-ideal transport mechanisms associated with the Δc (back-diffusion and water osmosis) have been taken into consideration. The COUN mode is a new exploration of the ED operating patterns to alleviate the detrimental effect of high Δc. It will provide a reference for designing and operating large-scale engineering projects for nutrient recovery by ED process and a trade-off among advanced ion removal, high-concentration limitation, and energy consumption.