Limited photon flux from the specimen using laser scanning microscopy during very short pixel dwell time often leads to insufficient signal-to-noise ratios (SNR). Increasing the SNR is invariably accompanied with a high power density, which may cause thermal damage to valuable specimens, for instance, the amber fossil record which provides an unparalleled insight into the history of terrestrial ecosystems over the past 230 million years. Here we describe an optimised high-resolution three-dimensional (3D) imaging strategy termed high dynamic range, colour structured illumination microscope (HDR-C-SIM) that overcomes the limitation of laser scanning confocal microscopy as well as the state-of-the-art micro-CT techniques for the study of amber inclusions. We demonstrate the utility of our new system for studying Mesozoic amber inclusions, which are difficult to image due to the optical properties of fossilised resin and the fossil's variable nature of preservation. Also, the HDR-C-SIM system was able to image the structural colours of cuckoo wasps preserved in mid-Cretaceous Burmese amber. By enabling palaeontologists to non-destructively study the nanostructures of organisms preserved in amber, HDR-C-SIM unlocks a new source of information about the palaeoecology of ancient ecosystems and holds promise for the non-destructive imaging of heat-sensitive samples in other fields.