Highly ordered MoS2/Mo-S-C nanoperiod multilayers are synthesized by a novel self-assembling mechanism in simultaneous sputtering of MoS2 and graphite targets. The sequential formation of MoS2-riched domain layers and Mo-S-C compositional mixed capping layers reveals no correspondence to the sample stage rotation but is caused by the low energy ion bombardment enhanced interdiffusion. The HRTEM observation shows that the phase segregation normal to the film surface is initiated from substrate-film interlayer with clear contrasts in the first few bi-layers, and then diffuses mutually in a quasiperiodic pattern between two altered sub-layers. Compared with sputtered MoS2 film, the bulk film of multilayers exhibit largely improved toughness under a normal load, and the preferential orientation of sputtered MoS2 in (002) basal planes is significantly enhanced, both of which render the film excellent loads-bearing capacity and lubricant properties. The nano-scratching tests performed on a nanoindentation system suggest that the nano-tribological performance of multilayers is directly determined by the altered structure and properties of neighboring sub-layers until stable tribofilms are formed. Meanwhile, the pin-on-disk tribotests in ambient air, low vacuum and high vacuum provide comparably low friction coefficient yet distinct wear lives in different atmospheres due to the partially restricted humid-sensitivity of sputtered MoS2 phase.