Biocemented　shale　soils　are　composite　materials,　and　their　micromechanical　properties　are　difficult　to　measure　using　common　macromechanical　tests.　In　this　work,　nanoindentation　tests　were　conducted　to　study　the　effects　of　microstructures,　crystal　types　of　calcium　carbonate,　and　locations　of　test　points　on　the　micromechanical　properties　of　biocemented　shale　soils.　The　transformation　process　of　crystal　types　of　calcium　carbonate　during　biogrouting　was　revealed　using　scanning　electron　microscopy　and　X-ray　diffraction　imaging　techniques.　The　results　showed　that　a　significant　amount　of　voids　within　the　cementing　body　were　generated　due　to　the　death　of　bacillus　pasteurii.　Vaterite　and　calcite　were　both　detected　in　the　same　sample,　where　the　vaterite　gradually　changed　into　calcite　during　the　biogrouting　process.　The　nanoindentation　tests　were　carried　out　in　locations　with　different　surrounding　conditions,　and　the　micromechanical　properties　of　biocemented　soils　were　obtained　through　analysis　of　the　load-displacement　curves.　The　relationships　between　fracture　toughness,　elastic　modulus,　and　hardness　were　found　to　be　linear　based　on　our　test　results.　The　established　empirical　relationships　help　understand　the　correlations　between　micromechanical　properties　and　also　provide　a　useful　method　for　the　characterization　of　fracture　toughness　of　biocemented　shale　soils.