Cracks are common faults in micro-electromechanical structures that affect the performance and dynamic behavior of the structure. Cracks can change the stiffness of the structure and parameters like resonance frequency, voltage and output power and after a specific time could lead to failure of that structure. Thus, diagnosis and identification the cracks in the structure will be very important. In the present study, a semi-analytical approach for the analysis of through the thickness cracks in the bimorph piezoelectric energy harvesters is proposed and both the stiffness reduction and changes in the capacitance of the structure due to through the thickness cracks are considered. From micromechanical point of view, a crack density based stress transfer method is employed for calculation of stiffness reduction due to crack formation in the middle layer. Analytical results of crack effects in mid-layer of a bimorph are derived by employing the Euler-Bernoulli beam theory assumptions and are validated via FEM. The effects of these defects on the mechanical parameters like resonance frequency, as well as electrical parameters like the output electrical power are discussed. It is observed that the presence of cracks in the mid-layer of bimorph piezoelectric energy harvester causes the decrease in its resonance frequency and the increase in the voltage and output power which is a sign of device failure. This work will provide an easy way for MEMS users to know some kinds of defects just only by monitoring the performance of the harvester.