The substrate effect on giant persistent photoconductivity (GPPC) of VO2 devices fabricated on the substrates of corning glass, Al2O3(0001), and TiO2(001) is investigated. Under the applied voltage within the hysteresis loop of voltage–current curve of the VO2 device, the GPPC is achieved by a short single pulse laser at laser intensity of 8.9 × 106 W m−2. The minimum laser pulse width (Wmin) to trigger GPPC in VO2 devices is found to be as small as 80 µs in the VO2 device fabricated on corning glass substrate. The magnitudes of Wmin for GPPC increase in the order of corning glass, TiO2, and Al2O3 substrates. The variation of the Wmin on each substrate is understood as the dissimilarity of thermal conductivity of each substrate. The minimum time required to induce GPPC (the incubation time) is estimated using 1D thermal transport model, which shows good qualitative agreement with experimental results.