Lateral thermoelectric devices, where the Peltier cooling and heating occur in a lateral direction, have shown promise for thermal management of on-chip hot spots, and because of the device orientation, thermoelectric materials with anisotropic properties such as holey silicon have shown even more promising cooling potential. However, the role of anisotropy in transient cooling and heating effects is little known, and thermal management optimization using a pulse has not been considered with anisotropic materials. Here, we study temporal and spatial interplays of Peltier, Joule, and Thomson effects in a holey silicon-based lateral thermoelectric device with varying pulse conditions and material properties. Our simulations show a supercooling effect, driven by Peltier cooling before Joule heating diffuses in, and that holey silicon with anisotropic thermal conductivities is favorable by delaying the diffusion in the lateral direction while allowing rapid heat dissipation in the vertical direction. Depending on the local temperature distribution, the Thomson effect is shown to strengthen the supercooling effect. A holey silicon-based thermoelectric device with a 1 kW · cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> hot spot shows temperature reductions from 117 °C to 102 °C in steady-state and temporarily to 100 °C with optimal pulse conditions. The transient cooling performance can be further improved by incorporating phase-change materials within holey silicon, in which their melting process delays a temperature overshoot. The anisotropy, specific heat, and latent heat play important roles in determining the transient cooling performance. Our findings show that lateral thermoelectric devices with anisotropic properties are promising for dynamic thermal management of on-chip hot spots.