The C1s binding energy spectra and total orbital momentum cross sections of small saturated alkanes (up to six carbons) and their isomers are investigated and used to differentiate their structural differences. The present study discovers that the impact of isomerization of alkanes on the carbon core shell is more significant than the elongation of the linear carbon chain. C1s binding energies are capable of serving as excellent indicators for isomers, whereas information on valence space such as valence binding energy spectra and valence momentum distributions is more sensitive to the length of the alkane chains. It further reveals that the terminal carbons exhibit smallest IPs for the alkanes but with a similar chemical environment as all their IPs are in the vicinity of 289.50 eV (±0.45 eV). The largest C1s chemical shift for the isomers is 0.88 eV (neopentane) which is nearly three times larger than the linear alkanes which is 0.30 eV. The inner valence bonding energy spectra clearly show a dependence on the number of carbons with a decreasing HOMO–LOMO energy gap of 9.91 eV for methane but 7.63 eV for hexane. The total momentum distributions are also proportional to the number of electrons but the isomers present small differences in the low momentum region which correspond to the long range in coordinate space.