The atmospheric pressure pulsed microwave He plasma jet has the advantages of high electron density and abundant active particles, but its shrinking on the discharge electrode morphology limits its application range. In order to modulate a He plasma jet with a longer plume and study its ionization development characteristics, we constructed a dual-channel pulsed microwave coaxial discharge device. He and air were, respectively, injected into the inner and outer gas channels of the resonator to generate a double-layer atmospheric pressure microwave plasma jet with a longer plume. It is observed that the bifurcation of the stratified plasma jet will occur by changing the gas flow. The ionization development of plasma jet was observed by using enhanced charge-coupled device and microwave Rayleigh scattering apparatus measured the space-time evolution of plasma and observed the three times ionization enhancement process of plasma jet development. The spectral lines of the active products associated with Penning ionization were observed by using a fiber optic spectrometer. A fluid model was constructed to simulate and analyze that under the condition of sufficient He flow rate (He flow rate is above 0.6 slm), there will be sufficient and stable He mole fraction (64%) at the stratification of the plasma jet. The experimental and simulation results show that the jet profile of the microwave He plasma is related to the inlet structure of the discharger and He flow rate. Stratified intake structure can produce stratified He plasma jet, and the unique appearance of bifurcation of jet can be produced by changing the flow rate of He. In the bifurcation process of the plasma jet, the product of Penning ionization inhibits the development of the main branch of the plasma jet, and the secondary electron avalanche of the local electric field promotes the formation of the branch of the plasma jet and is accompanied by the enhancement of the second ionization. The ionization mechanism of microwave He plasma is the resonance excitation of local enhanced electric field, the advance of ionizing waves, and the interaction between the spatially distributed active particles.