The thixotropic behaviors of ferrofluid samples of different particle concentration were studied using different measurement methods, including the three interval thixotropic test and the hysteresis loop test. The experimental results demonstrated that ferrofluids exhibit significant thixotropic behaviors and the microstructural evolution in ferrofluids behind the macroscopic rheological mechanics is discussed. The influence of magnetic field strength, particle concentration and temperature on the thixotropy of ferrofluids was also analyzed. Microscopic ferrofluid theory was adopted to study the thixotropic behaviors of ferrofluids under different shearing conditions, indicating that different thixotropic behaviors of ferrofluids can be induced by the presence and evolution of different kinds of microstructures, such as linear chain-like and dense drop-like structures. Furthermore, a phenomenal thixotropic model was employed to analyze the experimental results, indicating that a more specific model for ferrofluids is needed. These findings contribute to a better understanding of the microscopic mechanism of the complex rheological behaviors of ferrofluids.