Norditerpenoid alkaloids (NDA) are hexacyclic highly oxygenated compounds, and the analysis of their 3D configuration is important as it helps to interpret their bioactive conformations. High-performance liquid chromatography/atmospheric pressure chemical ionization mass spectrometry (LC/MS–APCI) is a promising technique to investigate NDA stereochemistry. The effect of the alpha (α)-substituent at carbon 1 and its configuration on the stability of NDA in the mass spectrometer was studied. It was observed that 1-OH NDA are more stable compared to 1-OMe NDA due to the intramolecular H-bonding that exists in 1-OH NDA. In addition, 1-epi-condelphine 9 was found to be less stable in the mass spectrometer compared to condelphine 7 as the nitrogen is no longer hydrogen-bonded to the β-hydroxyl at position 1, which highlights the importance of the substituent configuration at carbon 1.