In this paper, we investigate the influence of hypercapnia on the early and late phases of the phrenic neurogram using the matching pursuit (MP) method in the decebrated piglets. The phrenic neurogram was recorded from 8 piglets (4-7 days old) during control (40% O2 with 5% end-tidal CO2), the mild hypercapnia (40% O2 with 7% end-tidal CO2), and the severe hypercapnia (40% O2 with 15% end-tidal CO2). The time-frequency representations, atoms, of the phrenic neurogram are calculated from the 5 consecutive phrenic neurogram burst for each piglet for each condition using the MP method after vagotomy and chemodenervation. Our results show that the energy percentage of atoms representing the nonperiodic neural activities (NPNAs) significantly increased when the CO2 concentration was shifted from 7% to 15% in the early phase (the first half) of the phrenic neurogram. In addition, the energy percentage of atoms representing the periodic neural activities (PNAs) decreased in the late phase (the second half) when the CO2 concentration was shifted from 7% to 15% (p<0.01). As a summary, our result suggest that hypercapnia results in significant changes in the phrenic neurogram, an output of the respiratory neural networks in the medulla, both in time and frequency domians during early maturation.