The micro-Doppler (m-D) effect depends on the rotation of rotor blades in addition to the translation of the platform. Thus it is a characteristic for identifying small unmanned aerial vehicles (UAVs). However, compared with the Doppler signal induced by the translation of the platform, the m-D signal is weak. In this article, a highly localised dataassociation method, intrinsic synchrosqueezing analysis (ISA), is proposed for estimating m-D characteristics from the returned signal of small UAVs with a dual-channel radar. Employing synchrosqueezing transform on intrinsic mode functions derived from noiseassisted multivariate empirical mode decomposition, the proposed ISA method separates the Doppler signal and enables denoising and sharpening time-frequency representation of the m-D signal. Simulation results confirm the theoretical analysis, showing the feasibility of estimating m-D features in a noisy environment. Applications on field data illustrate brighter prospects for identifying small UAVs.This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.