The rational design of nanoheterostructured materials has attracted much attention because of its importance for developing highly efficient LIBs. Herein, we have demonstrated that internal Mo(6+) doped TiO2 nanocrystals in situ decorated with highly dispersed MoO3 clusters have been realized by a facile and rapid flame spray pyrolysis route for electrochemical energy storage. In such intriguing nanostructures, internal Mo(6+) doping can improve the conductivity of electrode materials and facilitate rapid Li(+) intercalation and ion transport and the heteroassembly of highly dispersed ultrafine MoO3 clusters with excellent electrochemical activity endows the TiO2 with extra Li(+) ion storage ability as well as incorporates Mo(6+). Thus, the as-prepared nanohybrid electrodes exhibit a high specific capacity and superior rate capability due to the maximum synergetic effect of TiO2, Mo(6+) and ultrafine MoO3 clusters. Moreover, the aerosol flame process with a unique temperature gradient opens a new strategy to design novel hybrid materials by the simultaneous doping and heteroassembly engineering for next-generation LIBs.