An experimental study of the afterglow mode was performed with a third generation electron cyclotron resonance ion source, SECRAL-II (Superconducting ECR ion source with Advanced design in Lanzhou No. II), under double frequency heating. The experimental results show that intense pulsed beams of highly charged ions (e.g., $266\text{ }\text{ }\mathrm{e}\ensuremath{\mu}\mathrm{A}$ of ${^{129}\mathrm{Xe}}^{34+}$ and $169\text{ }\text{ }\mathrm{e}\ensuremath{\mu}\mathrm{A}$ of ${^{129}\mathrm{Xe}}^{38+}$) could be produced at high frequency ($24+18\text{ }\text{ }\mathrm{GHz}$) and high power ($\ensuremath{\sim}8\text{ }\text{ }\mathrm{kW}$), even compared with the beam intensity records of SECRAL-II obtained in continuous wave (cw) mode at higher microwave frequency ($28+18\text{ }\text{ }\mathrm{GHz}$) and higher power ($\ensuremath{\sim}10\text{ }\text{ }\mathrm{kW}$), the gain factor is also up to $\ensuremath{\sim}3$. Meanwhile, it is found that the afterglow decay time in our study is much longer than that obtained with the second generation ECR ion sources typically operating at 10--18 GHz, and the corresponding peak duration is greater than 2 ms. This study provides a viable solution for heavy ion synchrotron accelerator complex such as High Intensity Heavy Ion Accelerator Facility project that requires intense pulsed beams of highly charged ions with long peak duration.