The quantum conductance of the quantum dots (QDs) made of two kinds of primary carbon nanotubes (CNTs), i.e., armchair and zigzag CNTs, threaded by an axial magnetic field, has been studied by using the tight binding approximation and constant interaction model. It is found that under increasing axial magnetic field, each conductance shell of the zigzag CNT-QDs could split into two groups with each group of two peaks moving up or down, respectively. And the up- and down-moving two peaks would re-group with other two peaks, down- and up-moving, in the neighboring shell, forming a new four-peak shell, and then re-splitting, re-grouping again due to the Aharonov–Bohm effect, which is in agreement with those of experiments. But, in contrast, the conductance shells of the armchair CNT-QDs do not split by the magnetic field. Our subsequent theoretical studies show further that the above phenomena, i.e., the conductance shell-splitting, re-grouping, and re-splitting again with increasing the magnetic field exist in all the CNT-QDs except for the armchair one.