We describe dynamic modes that originate from shape and structure fluctuations in a droplet microemulsion system. The modes are decoupled by a contrast variation neutron scattering technique using the relative intermediate form factor method. The strategy of the method is analogous to the relative form factor method, which decouples the form and structure factors from the small-angle neutron scattering intensity [M. Nagao, Phys. Rev. E 75, 061401 (2007)]. First, we will briefly explain theoretical and experimental approaches to understanding neutron spin echo (NSE) data from droplet microemulsion systems. Then we will introduce the relative intermediate form factor method, which decouples shape and structure fluctuations. The concentration dependence of the droplet dynamics in a microemulsion system is used to elucidate the strengths of this method. The intermediate form and structure factors are successfully decoupled from an observed intermediate scattering function by NSE. The decay rate of the shape fluctuation modes linearly decreases, while the fluctuation amplitude increases as the droplet concentration increases. The first cumulant of the obtained intermediate structure factor shows a clear de Gennes narrowing behavior at a length scale corresponding to the interdroplet distance. However, in the high-momentum-transfer and longer-time regions, the first cumulant deviates from the intermediate structure factor. This result suggests the existence of other dynamic modes of structure fluctuations rather than the center-of-mass diffusion mode.