Rational harmonic mode-locking refers to a mode-locking state achieved at the modulation frequency that doesn’t match the fundamental frequency. In this paper, we investigated and experimentally achieved rational harmonic mode-locking in optoelectronic oscillators (OEO) for the first time through three schemes based on electric amplitude modulator (AM), electric phase modulator (PM), and Mach-Zehnder modulator (MZM), respectively. In the experiment, the fundamental frequency mode-locking as well as the 2nd-order, 3rd-order, and 4th-order rational harmonic mode-locking were obtained, all generating ultrashort microwave pulses with a repetition rate of 95 kHz and a carrier frequency of 10 GHz. Subsequently, the characteristics of the pulse signals generated by different schemes, such as pulse width, pulse amplitude, and spectral width, were systematically investigated. By comparison, we found that the AM-based mode-locked OEO generates microwave pulse signals with higher stability and narrower pulse width; the PM-based mode-locked OEO can excite more longitudinal modes in the cavity but generates signals with more spurious noise; the MZM-based mode-locked OEO has a simple structure and requires lower power of the modulation signal. We believe this paper could provide some reference for the research on the physical mechanism of the mode-locking phenomenon generated in the OEO when the modulation frequency is mismatched.