It is well know that the internal flow field and nozzle geometry affected the spray behavior, but without high-speed microscopic visualization, it is difficult to characterize the spray structure in details. Single-hole diesel injectors have been used in fundamental spray research, while most direct-injection engines use multi-hole nozzle to tailor to the combustion chamber geometry. Recent engine trends also use smaller orifice and higher injection pressure. This paper discussed the quasi-steady near-nozzle diesel spray structures of an axisymmetric single-hole nozzle and a symmetric two-hole nozzle configuration, with a nominal nozzle size of 130 μm, and an attempt to correlate the observed structure to the internal flow structure using computational fluid dynamic (CFD) simulation. The test conditions include variation of injection pressure from 30 to 100 MPa, using both diesel and biodiesel fuels, under atmospheric condition. The imaging technique utilizes a 150 pico-second synchrotron-based Ultrafast Phase-contrast X-ray in order to freeze-capture the fast moving jet and achieve excellent spatial resolution in order to compare the wavy jet structure. Both nozzle holes originate from a sac of identical geometry, but different flow structure inside the nozzle cause significant difference in the observed flow structure near the nozzle exit. The ultrafast fast images revealed unique surface and internal morphology of the fuel sprays that can be identified. The two-hole nozzle produces much more unstable jet structure under same injection conditions. The early wavelength developed in the jet is measured to be on the order of 30~80 μm, with the frequency range of 5 to 10 MHz, depending on the injection conditions up to 60 MPa injection pressure when the wavelength analysis is still feasible. The differences between the nozzle configurations are investigated using CFD simulation. The results show that the three-dimensional fluid flow entering the two-hole nozzle generates stronger streamline curvature and stream-wise counter-rotational vortices which are by default absent in the axisymmetric single-hole nozzle. It also produces thicker shear layer and higher turbulence. The interactions of downwash entrance flow with turbulence potentially enhance the instability and produce wider spray cone angles.