We studied the structure development in the dewetting process of deuterated polystyrene (dPS) and poly(vinyl methyl ether) (PVME) thin films, which were prepared by a spin-coating method on a quartz substrate, after the temperature jump into the two-phase region, using time-resolved specular and off-specular neutron reflectivity (NR), specular X-ray reflectivity (XR), light scattering (LS), andoptical microscope (OM) measurements. The OM and specular XR measurements showed that there clearly existed an incubation period before dewetting. In the incubation period, composition fluctuations between dPS and PVME were developed due to phase separation. The specular NR results revealed that composition fluctuations began to occur just after the temperature jump along the depth direction over the film, giving rise to the composition gradient heterogeneously over the film. Composition fluctuations were also observed in the in-plane direction by the off-specular NR and LS measurements: the off-specular NR measurements revealed that composition fluctuations with micrometer scale in the M-plane direction occurred in the incubation period, and they also grew up with the annealing time before dewetting, implying composition fluctuations induced dewetting, while the LS measurements detected only droplet formation of dewetting. On the basis of the off-specular NR results, the inside structure of the dewetting was additionally discussed, showing tilted structure along the depth direction.