Small molecules such as molecular oxygen, nitric oxide, and carbon monoxide play important roles in life, and many proteins require the transport of small molecules to and from the bulk solvent for their function. Ligand migration within a protein molecule is expected to be closely related to the overall structural changes of the protein, but the detailed and quantitative connection remains elusive. For example, despite numerous studies, how occluded ligand migration affects the kinetics and structural dynamics of the R-T transition remains unclear. To shed light on this issue, we chose homodimeric hemoglobin (HbI) with the I114F mutation (I114F), which is known to interfere with ligand migration between the primary and secondary docking sites, and studied its kinetics and structural dynamics using time-resolved X-ray solution scattering. The kinetic analysis shows that I114F has three structurally distinct intermediates (I-1 I-2, and I-3) as in the wild type (WT), but its geminate CO recombination occurs directly from I-1 without the path via I-2 observed in WT. Moreover, the structural transitions, which involve ligand migration (the transitions from I-1 to I-2 and from I-3 to the initial state), are decelerated compared to WT. The structural analysis revealed that I114F involves generally smaller structural changes in all three intermediates compared to WT.