Forward osmosis (FO) technology has the merit potential to remove heavy metal ions from wastewater. However, the deficiency of FO membranes with low selectivity and permeability has hampered the scale-up and development of this technology. In this work, we coated a hydrophilic alginate/Ca2+ thin layer through the layer-by-layer (LbL) assembly as an interlayer on polyethersulfone (PES) microfiltration (MF) substrate to enhance the separation performance of the thin-film composite (TFC) membrane. The interlayer thickness was controlled by the LbL cycles (1–7 cycles), and its effect on surface properties of substrates in terms of hydrophilicity and pore size was investigated thoroughly. Then the influence of interlayer LbL cycles on the polyamide (PA) synthesis through interfacial reaction was studied. Results show that the interlayer prevents the PA layer's intrusion into the substrate pores and provides a hydrophilic and smooth surface to synthesize a defect-free PA layer. SEM images show that a dense, uniform, and defect-free PA rejection layer was formed on interlayer-coated MF substrates. FO performance result also verified the positive effect of interlayer on TFC membrane performance, where TFC-LbL.5 membrane (with 5 LbL cycles of alginate/Ca2+) showed 2 times higher water flux than control TFC membrane (23.3 LMH compared to 9.2 LMH). In the TFC-LbL.5 membrane, the defect-free PA active layer formed on the alginate/Ca2+ interlayer acted as a favorable barrier for different heavy metal ions (Cr3+, Co2+, and Hg2+) with the rejection of more than 99% under FO mode. This work offers a novel opportunity for the practical construction and development of high-efficiency TFC-FO membranes for heavy metal removal applications.