In order to increase the loading of rare earth- and molybdenum-rich high-level waste in the waste forms, zirconolite- and powellite-based multi-phase borosilicate glass-ceramics were synthesized via an in-situ heat treatment method. The effects of the CTZ (CaO, TiO2 and ZrO2) content on the crystallization, microstructure and aqueous durability of the multi-phase borosilicate glass-ceramics were studied. The results indicate that the increase of CTZ content can promote crystallization. The glass-ceramics presented even structures when the CTZ content was ≥ 40 wt%. For the glass-ceramic with 40 wt% CTZ, only zirconolite and powellite crystals were detected and powellite crystals were mainly distributed around zirconolite, whereas for the glass-ceramics with 50 wt% CTZ, perovskite was detected. Furthermore, the leaching rates of Na, Ca, Mo and Nd were in the ×10−3, ×10−4, ×10−3 and ×10−5 g·m−2·d·−1 orders of magnitude on the 28th leaching day, respectively.