To provide a structure refining apparatus, a method and a program capable of univocally and appropriately setting a restraint with a statistically feasible intensity and specifying a crystal structure model making use of a measurement result under a constraint condition to reasonable known data. A structure refining apparatus 100 adjusting the crystal structure model on the basis of the measurement result and the known data includes a restraint applying unit 120 configured to apply the restraint such that a divergence between a parameter specifying a crystal structure and a known representative value becomes equivalent to a standard uncertainty of the known representative value and a structure specifying unit 140 configured to specify the crystal structure model on the basis of the measurement result under the applied restraint.