Accurate prediction of hypersonic boundary-layer transition plays an important role in thermal protection system design of hypersonic vehicles. Restricted by the capability of spatial diagnostics for hypersonic boundary-layer study, quite a lot of problems of hypersonic boundary-layer transition, such as nonlinearity and receptivity, remain outstanding. This work reports the application of focused laser differential interferometer to instability wave development across hypersonic boundary-layer on a flared cone model. To begin with, the focused laser differential interferometer is designed and set up in a Mach number 6 hypersonic quiet wind tunnel with the focal point in the laminar boundary-layer of a 5 degree half-angle flared cone model. Afterwards, instability experiments are carried out by traversing the focal point throughout the hypersonic boundary-layer and the density fluctuation along the boundary-layer profile is measured and analyzed. The results show that three types of instability waves ranging from 10 kHz to over 1 MHz are co-existing in the hypersonic boundary-layer, indicating the powerful capability of focused laser differential interferometer in dynamic response resolution for instability wave study in hypersonic flow regime; furthermore, quantitative analyses including spectra and bicoherence analysis of instability waves throughout the hypersonic boundary-layer for both cold and heated cone models are performed.