In this paper, the flow patterns during water flow boiling instability in pin-fin microchannels were experimentally studied. Three types of pin-fin arrays (in-line/circular pin-fins, staggered/circular pin-fins, and staggered/square pin-fins) were used in the study. The flow instability started to occur as the outlet water reached the saturation temperature. Before the unstable boiling, a wider range of stable boiling existed in the pin-fin microchannels compared to that in the plain microchannels. Two flow instability modes for the temperature and pressure oscillations, which were long-period/large-amplitude mode and short-period/small-amplitude mode, were identified. The temperature variation during the oscillation period of the long-period/large-amplitude mode can be divided into two stages: increasing stage and decreasing stage. In the increasing stage, bubbly flow, vapor-slug flow, stratified flow, and wispy flow occurred sequentially with time for the in-line pin-fin microchannels; liquid single-phase flow, aforementioned four kinds of two-phase flow patterns, and vapor single-phase flow occurred sequentially with time for the staggered pin-fin microchannel. The flow pattern transitions in the decreasing stage were the inverse of those in the increasing stage for both in-line and staggered pin-fin microchannels. For the short-period/small-amplitude oscillation mode, only the wispy flow occurred. With the increase of heat flux, the wispy flow and the vapor single-phase flow occupied more and more time ratio during an oscillation period in the in-line and staggered pin-fin microchannels.