There are currently five different kinds of transcranial magnetic stimulation (TMS) motor mapping algorithms available, from ordinary point-based algorithms to advanced field-based algorithms. However, there have been only a limited number of comparison studies conducted, and they have not yet examined all of the currently available algorithms. This deficiency impedes the judicious selection of algorithms for application in both clinical and basic neuroscience, and hinders the potential promotion of a potential superior algorithm. Considering the influence of algorithm complexity, further investigation is needed to examine the differences between fMRI peaks and TMS cortical hotspots that were identified previously. Twelve healthy participants underwent TMS motor mapping and a finger-tapping task during fMRI. The motor cortex TMS mapping results were estimated by five algorithms, and fMRI activation results were obtained. For each algorithm, the prediction error was defined as the distance between the measured scalp hotspot and optimized coil position, which was determined by the maximum electric field strength in the estimated motor cortex. Additionally, the study identified the minimum number of stimuli required for stable mapping. Finally, the location difference between the TMS mapping cortical hotspot and the fMRI activation peak was analyzed. The projection yielded the lowest prediction error (5.27 ± 4.24 mm) among the point-based algorithms and the association algorithm yielded the lowest (6.66 ± 3.48 mm) among field-based estimation algorithms. The projection algorithm required fewer stimuli, possibly resulting from its suitability for the grid-based mapping data collection method. The TMS cortical hotspots from all algorithms consistently deviated from the fMRI activation peak (20.52 ± 8.46 mm for five algorithms). The association algorithm might be a superior choice for clinical applications and basic neuroscience research, due to its lower prediction error and higher estimation sensitivity in the deep cortical structure, especially for the sulcus. It also has potential applicability in various other TMS domains, including language area mapping and more. Otherwise, our results provide further evidence that TMS motor mapping intrinsically differs from fMRI motor mapping.