We define the spatial clustering of X-rays within Jupiter’s northern auroral regions by classifying their distributions into ‘X-ray auroral structures’. Using data from Chandra during Juno’s main mission observations (24 May 2016 – 8 September 2019), we define five X-ray structures based on their ionospheric location and calculate the distribution of auroral photons. The morphology and ionospheric location of these structures allow us to explore the possibility of numerous X-ray auroral magnetospheric drivers. We compare these distributions to Hubble Space Telescope (HST)and Juno (Waves and MAG) data, and a 1D solar wind propagation model to infer the state of Jupiter’s magnetosphere. Our results suggest that the five sub-classes of ‘X-ray structures’ fall under two broad morphologies: fully polar and low latitude emissions. Visibility modelling of each structure suggests the non-uniformity of the photon distributions across the Chandra intervals are likely associated with the switching on/off of magnetospheric drivers as opposed to geometrical effects. The combination of ultraviolet (UV) and X-ray morphological structures is a powerful tool to elucidate the behaviour of both electrons and ions and their link to solar wind/magnetospheric conditions in the absence of an upstream solar monitor.