Background: Quantitative activity estimation is essential in nuclear medicine imaging. Mismatch between SPECT and CT images at the same imaging time point due to patient movement degrades accuracy in both diagnostic studies and target radionuclide therapy dosimetry. This work aims to study the mismatch effects between CT and SPECT data on attenuation correction (AC), volume-of-interest (VOI) delineation, and registration for activity estimation. Methods: Nine 4D XCAT phantoms were generated at 1, 24, and 144 h post In-111 Zevalin injection, varying in activity distributions, body sizes, and organ sizes. Realistic noisy SPECT projections were generated by an analytical projector and reconstructed with a quantitative OS-EM method. CT images were shifted, corresponding to SPECT images at each imaging time point, from -5 to 5 voxels and also according to a clinical reference. The effect of mismatched AC maps was evaluated using mismatched CT images for AC in SPECT reconstruction while VOIs were mapped out from matched CTs. The effect of mismatched VOI drawings was evaluated using mismatched CTs to map out target organs while using matched CTs for AC. The effect of mismatched CT images for registration was evaluated by registering sequential mismatched CTs to align corresponding SPECT images, with no AC and VOI mismatch. Bi-exponential curve fitting was performed to obtain time-integrated activity (TIA). Organ activity errors (%OAE) and TIA errors (%TIAE) were calculated. Results: According to the clinical reference, %OAE was larger for organs near ribs for AC effect. For VOI effect, %OAE was larger for small and low uptake organs. For registration effect, %TIAE were larger when mismatch existed in more numbers of SPECT/CT images, while no substantial difference was observed when using mismatched CT at different imaging time points as registration reference. %TIAE was highest for VOI, followed by registration and AC, e.g., 20.62%±8.61%, 9.33%±4.66% and 1.13%±0.90% respectively for kidneys. Conclusions: The mismatch between CT and SPECT images poses a significant impact on the accuracy of quantitative activity estimation, attributed particularly from VOI delineation errors. It is recommended to perform registration between emission and transmission images at the same time point to ensure diagnostic and dosimetric accuracy.