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Utilization of mussel shell as a construction material has a promising application potential to meet the challenges of mussel shell wastes treatment in coastal cities. However, the inferior mechanical properties of mussel shell aggregate concrete (MSAC) has restricted its wider promotion in high performance applications due to the inferior properties of mussel shell aggregate (MSA) and the poor interface bonding behavior between MSA and mortar. To improve the mechanical properties of MSAC with a MSA replacement ratio of 30%, this study focused on the mixture proportions design of MSAC by particle size optimization of MSA and compact packing of raw materials, and the MSA modification by polymer-cement paste composite and microbial induced carbonate precipitation. Microstructure tests were conducted to provide an insight into the mechanism behind the improved mechanical properties of MSAC. The results exhibit that, both of mixture design and aggregate modification, have beneficial effects on improving the compressive strength and splitting tensile strength of MSAC. The enhancement mechanism of MSAC mechanical properties can be explained by the enhancement in the microstructure of MSAC, i.e. the increased compactness of MSA-mortar interface and the refined pore structure of mortar.