Many existing studies on manifold microchannels assume steady, spatially uniform heat fluxes, which do not adequately represent localized hotspots under pulsed heating in electronic chips. However, quantitative studies of the interplay between hotspot location and pulse duration in Z-type manifold microchannel heat sinks remain limited. In this study, a three-dimensional transient conjugate heat transfer model for single-phase flow is developed to investigate the timescale dependence of hotspot-location effects in a Z-type manifold microchannel heat sink. A localized square-wave heat-flux pulse is superimposed on a steady, spatially uniform background heat flux, and five hotspot locations spanning different local branch flow rates are considered. The transient thermal impedance at the hotspot and a hotspot-location sensitivity metric are defined. The critical pulse duration is then determined as the duration at which the hotspot-location sensitivity exceeds a specified engineering threshold.The transition of the hotspot response from solid thermal-storage dominance to local convective-cooling dominance is elucidated by analyzing the branch mass flow rates, the correlation between flow rate and thermal impedance, and the transient partitioning of energy between storage in the solid and removal by the coolant. The results show that, when the pulse duration is less than approximately 0.1 times the reference thermal time constant, the differences in peak dynamic thermal impedance among the hotspot locations remain below 3%, and the hotspot response is governed primarily by thermal diffusion and energy storage in the solid. When the pulse duration reaches approximately 0.6 times the reference thermal time constant, the location sensitivity exceeds the engineering threshold of 5% and gradually approaches a plateau with increasing pulse duration. Under long-pulse conditions, the location sensitivity is expected to reach approximately 18%. The hotspot adjacent to the low-flow-rate branches exhibits the highest peak temperature rise, with a dynamic thermal impedance approximately 15% higher than that at the high-flow-rate location. These findings provide a timescale-based criterion for determining whether hotspot location should be incorporated into the design of manifold microchannel heat sinks subjected to dynamic thermal loads.