This study proposes using membrane distillation (MD) as an alternative to the conventional multi-stage flushing (MSF) process to concentrate a semi-product of organic fertilizer. By applying a unique asymmetric polyvinylidene fluoride (PVDF) membrane, which was specifically designed for MD applications using a nonsolvent thermally induced phase separation (NTIPS) method, the direct contact membrane distillation (DCMD) performance was investigated in terms of its sustainability in permeation flux, fouling resistance, and anti-wetting properties. It was found that the permeation flux increased with increasing flow rate, while the top-surface facing feed mode was the preferred orientation to achieve 25% higher flux than the bottom-surface facing feed mode. Compared to the commercial polytetrafluoroethylene (PTFE) membrane, the asymmetric PVDF membrane exhibited excellent anti-fouling and sustainable flux, with less than 8% flux decline in a 15 h continuous operation, i.e., flux decreased slightly and was maintained as high as 74 kg·m−2·h−1 at 70 °C. Meanwhile, the lost flux was easily recovered by clean water rinsing. Overall 2.6 times concentration factor was achieved in 15 h MD operation, with 63.4% water being removed from the fertilizer sample. Further concentration could be achieved to reach the desired industrial standard of 5x concentration factor.