Attention on semiconductor nanocrystals have been largely focused because of their unique optical and electrical properties, which can be applied as light absorber and luminophore. However, the band gap and structure engineering of nanomaterials is not so easy because of their finite size. Here we demonstrate an approach for preparing ternary AgInS2 (AIS), quaternary AgZnInS (AZIS), AgInS2/ZnS and AgZnInS/ZnS nanocompounds based on cation exchange. First, pristine Ag2S quantum dots (QDs) with different sizes were synthesized in one-pot, followed by the partial cation exchange between In(3+) and Ag(+). Changing the initial ratio of In(3+) to Ag(+), reaction time and temperature can control the components of the obtained AIS QDs. Under the optimized conditions, AIS QDs were obtained for the first time with a cation disordered cubic phase and high photoluminescence (PL) quantum yield (QY) up to 32% in aqueous solution, demonstrating the great potential of cation exchange in the synthesis for nanocrystals with excellent optical properties. Sequentially, Zn(2+) ions were incorporated in situ through a second exchange of Zn(2+) to Ag(+)/In(3+), leading to distinct results under different reaction temperature. Addition of Zn(2+) precursor at room temperature produced AIS/ZnS core/shell NCs with successively enhancement of QY, while subsequent heating could obtain AZIS homogeneous alloy QDs with a successively blue-shift of PL emission. This allow us to tune the PL emission of the products from 483 to 675 nm and fabricate the chemically stable QDs core/ZnS shell structure. Based on the above results, a mechanism about the cation exchange for the ternary nanocrystals of different structures was proposed that the balance between cation exchange and diffusion is the key factor of controlling the band gap and structure of the final products. Furthermore, photostability and in vitro experiment demonstrated quite low cytotoxicity and remarkably promising applications in the field of clinical diagnosis.