A low carbon bainitic steel with microstructure of granular bainite (GB), acicular ferrite (AF), and bainitic ferrite (BF) is obtained under different deformation and cooling rate. The effect of deformation and cooling rate on microstructural characteristics such as the type of the matrix, the size, and area fraction of the martensite–austenite (M–A) constituents is investigated. In addition, the nanohardness of these three kinds of matrix as well as that of the M–A constituents in them is characterized. Further, the effect of matrix and M–A constituents on strength–toughness balance is studied. Results indicate that deformation expands the transformation region. The size as well as the area fraction of the M–A constituent decreases with the increasing of the cooling rate. After deformation, the area fraction of the M–A constituents increases. Nanohardness of GB, AF, and BF increases orderly, but that of the M–A constituents in them decreases accordingly. The nanohardness of the M–A constituent is significantly affected by its carbon concentration. AF is the optimum microstructure having superior strength–toughness balance.