Tunable and enhanced low-field magnetoresistance (LFMR) is observed in epitaxial (La0.7Sr0.3MnO3)(0.5):(ZnO)(0.5) (LSMO:ZnO) self-assembled vertically aligned nanocomposite (VAN) thin films, which have been grown on SrTiO3 (001) substrates by pulsed laser deposition (PLD). The enhanced LFMR properties of the VAN films reach values as high as 17.5% at 40 K and 30% at 154 K. They can be attributed to the spin-polarized tunneling across the artificial vertical grain boundaries (GBs) introduced by the secondary ZnO nanocolumns and the enhancement of spin fluctuation depression at the spin-disordered phase boundary regions. More interestingly, the vertical residual strain and the LFMR peak position of the VAN films can be systematically tuned by changing the deposition frequency. The tunability of the physical properties is associated with the vertical phase boundaries that change as a function of the deposition frequency. The results suggest that the tunable artificial vertical GB and spin-disordered phase boundary in the unique VAN system with vertical ferromagnetic-insulating-ferromagnetic (FM-I-FM) structure provides a viable route to manipulate the low-field magnetotransport properties in VAN films with favorable epitaxial quality.