The effect of processing histories (fluxing and pre-annealing) on the amorphous structure and the crystallization kinetics of amorphous Fe40Ni40P14B6 alloy prepared by melt spinning has been studied by differential scanning calorimetry, X-ray diffraction, transmission and scanning electron microscopy. For isothermal crystallization, an incubation time exists, and for isochronal crystallization, an abnormally sharp crystallization peak (with the transformed fraction corresponding to the transformation-rate maximum f(p) as less than 0.632) occurs. Subjected to fluxing and pre-annealing, the incubation time (in isothermal crystallization) decreases, whereas the initial crystallization temperature (in isochronal crystallization) declines as well as the less sharp crystallization peak and f(p) approaches 0.632. A kinetic model considering transient nucleation is proposed and analyzed, which could describe well the singular crystallization behavior of amorphous Fe40Ni40P14B6 alloy. A recipe based on the kinetic model is also proposed to obtain the kinetic parameters from experiment data. Via kinetic analysis and amorphous structural characterization, it is considered that pre-annealing and fluxing promote relaxation of the system close to the meta-stable equilibrium state; the atomic structure becomes more similar to the correspondingly crystallized phase, thus declining the amorphous stability and alleviating the transient effect on nucleation.