Online estimation of instantaneous frequencies is a method to treat information signals by following a set of certain algorithm for the purpose of extracting the sine wave signal frequency that is overwhelmed in the noise. Among several algorithms available nowadays, two are selected here-one is the modification of Rife (MRife) algorithm based on frequency-domain analysis; and the other is the correlation series based (CSB) algorithm. With simulation methods, the estimation error, stabilization time and computation load of these two algorithms are analyzed and compared respectively. Finally, these two algorithms are applied to estimate the vibration signal frequency of the diesel engine’s base under normal operating conditions. From the results, we come to the conclusion that MRife algorithm and CSB algorithm both have their specific advantages, whereas MRife algorithm is more applicable in the view of estimation error.