An ECU, as a combustion system control device, includes various control units such as a first estimation unit, a second estimation unit, a comparison/selection unit, and an injection control unit. The first estimation unit estimates, as a first estimation value, the mixing ratio of each molecular structure species contained in fuel based on the value detected by an in-cylinder pressure sensor that is a combustion sensor. The second estimation unit estimates, as a second estimation value, the above mixing ratio based on the values detected by a density sensor and a dynamic viscosity sensor that are property sensors. The comparison/selection unit compares the first estimation value with the second estimation value to select an estimation value with higher estimation accuracy, and various control units such as the injection control unit control the operation of a combustion system by using the selected estimation value.