The n-type hydrogenated nanocrystalline silicon oxide (nc-SiOx:H) layers were prepared by 13.56 MHz radio frequency (RF) plasma-enhanced chemical vapor deposition (PECVD). The effects of CO2 and PH3 gas flow variation on the layer performance were investigated in advance. The increase of CO2 flow rate could enhance the oxygen content (CO) in nc-SiOx:H, leading to a decrease of crystallinity (XC), which would induce a nanocrystalline to amorphous phase transition. When a small amount of PH3 was added, XC increased surprisingly. The analysis demonstrated that the incorporation of phosphorous suppressed CO in the layer although it could also induce the nanocrystalline to amorphous phase transition. It was the CO reduction that made the layer crystallize more easily. As a result, the maximum XC could be obtained with a moderate PH3 flow rate. Nevertheless, the PH3 flow rate could still be increased further in order to get the highest dark conductivity (σd). Over this point, excessive PH3 would make σd decrease gradually, which could be attributed to that the increase of the amorphous phase reduced the effective doping efficiency of phosphorus. Both the CO reduction and the phase transition from nanocrystalline to amorphous could result in the decrease of the optical bandgap (E04). The synergistic effect of CO2 and PH3 indicated that it was important to adjust CO2 and PH3 flow rates together for preparing the nc-SiOx:H layer with both high transparency and high conductivity.