The advanced treatment of proprietary Chinese medicine secondary effluent (PCMSE) was strongly needed with the recent implementation of a more stringent discharge standard. Based on the features of PCMSE and the reuse of Al3+from wastewater from soaking of Pinellia Ternata with alumen (WSPTA), three new combined processes were designed for the advanced treatment of PCMSE on a larger pilot scale. A pilot scale study showed that compared with two other combined processes, the new coupling of a biological-aerated filter with Al3+ addition (BAFA)-O3/H2O2 with microbubble (OHOMB) (CBAFAOHOMB) obtained the maximum pollutant removal (with removals of 91.71%, 94.64%, and 82.32% being observed for color, total phosphorus (TP), and chemical oxygen demand (COD), respectively) and acquired the lowest Al3+residual in the effluent. During CBAFAOHOMB treatment of PCMSE, the vast majority of TP elimination, 35.20% of COD removal, and 49.40% of color removal were achieved by BAFA; OHOMB obtained 64.80% of COD removal and 60.60% of color removal, and biofilm activity in BAFA slightly changed under a 10 mg/L Al3+ dose. Furthermore, microbubble aeration was more efficient in removing organics than conventional bubble aeration during O3/H2O2 oxidation, and suspended solid (SS) relatively significantly lowered oxidation ability in the OHOMB system. These results indicated that CBAFAOHOMB markedly integrated advantages of BAFA and OHOMB, and was a proposed process for the advanced treatment of PCMSE. Meanwhile, it was feasible that WSPTA was reused for PCMSE treatment as an Al3+ source.