In diesel engines, double-layer multi-holes nozzles contribute significantly in making spray injection uniform in both the circumferential and axial directions; they further ensure that minimal or no interactions are encountered among the spray jets emerging from the nozzle holes and positively affect fuel atomisation and enhance mixing during engine operation. In this study, the variation in internal flow characteristics and spray patterns from the upper and the lower layer nozzle holes were investigated experimentally and computationally. A double-layer 8-hole heavy-duty diesel engine injector nozzle was utilised for the characterisation of hole-to-hole variation on spray formation. The actual nozzle geometry was derived from X-ray scans obtained at the third generation X-ray imaging and biomedical beamline station in SSRF, revealing all geometrical differences between the individual injection holes. The momentum fluxes from each holes were obtained together with spray tip penetration under non-evaporating conditions. These data were used to validate the computational fluid dynamics (CFD) model suitable to describe the relevant flow processes. Initially, an Eulerian-Eulerian two-phase flow model was utilised to predict the internal nozzle flow under cavitating conditions. This model was weakly coupled with a Lagrangian spray model predicted the subsequent atomisation and penetration of all individual spray plumes. The results show that cavitation development within the upper layer holes is more intense than those formed within the lower layer nozzle holes; this is leading to higher injection rates from the lower layer nozzle holes that they also exhibit less cycle-to-cycle variations in the observed spray patterns.