On the basis of the synergistic strategy of lacunary polyoxometalate structure-directing function and chiral ligand inducting role, two pairs of enantiomeric polyoxotungstates, (NH4)4(TMA)4[Zr4(μ3-O)2(l-/d-mal)2(B-α-HSiW10O37)2] (TMA = tetramethylammonium, mal = malate (C4H5O5); l-mal for 1a, d-mal for 1b) and (NH4)4(TMA)4[Zr4(μ3-O)2(l-/d-mal)2(B-α-PW10O37)2] (l-mal for 2a, d-mal for 2b), and a mesomeric polyoxotungstate, (NH4)3Na2K5[Zr4(μ3-O)2(l-mal)(d-mal)(B-α-SiW10O37)2] (3), were hydrothermally synthesized. 1a, 2a and 1b, 2b respectively exhibit 1-D 21 right- and left-hand helical chains formed by hydrogen-bonding interactions, and 3 forms a 3-D (3,10)-connected framework by Na+/K+ ions with {418.624.83}{43}2 topology. These homochiral compounds represent the first examples of enantiomerically pure ZrIV-substituted Keggin POMs. In this system, {Zr4(μ3-O)2(l-/d-mal)2} clusters transfer chirality from d- or l-mal to Keggin polyoxotungstate dimeric clusters, which was demonstrated by structural comparison between the homochiral architecture and mesomer as well as circular dichroism spectra of enantiomers. UV-vis diffuse reflectance spectra reveal that 1-3 are potential semiconductor materials. In addition, 1 and 2 exhibit second harmonic generation response with their response intensities of 0.8 times that of KDP.