Fluid migration in subduction zones is a key controlling factor of slow and megathrust earthquakes at plate boundaries. During the migration, seismic velocity and heterogeneous structures in its pathways may be temporarily varied, preferably triggering slow earthquakes. Here, we show that transient changes of seismic heterogeneity occurred 0-9 months before shallow slow earthquakes in the Nankai subduction zone, Japan, using very long-term (6–10 y) records of ambient seafloor noise. The heterogeneity changes preceding to shallow slow earthquakes were observed near the margin of the source region, while concurrent changes primarily occurred in the source region. We propose that the heterogeneity changes are attributed to dynamic fluid migration, and the difference in timings reflects the pore pressure level in the corresponding source region. When fluids are supplied to a source region under relatively low pressure, fluids are leaked out from its downdip or updip side, and slow earthquakes occur not immediately but with a time delay of at most 9 months. In the high pore pressure case, slow earthquakes occur immediately with fluid migration from the source region. This study suggests that the heterogeneous seismic structure is possibly changed by fluid migration before slow earthquakes in the Nankai subduction zone.