Miniaturized bionic compound eyes featured with multi-aperture imaging have potential applications in the areas of micro opto-electro-mechanical-system. In this manuscript, we present a novel structure of the bionic compound eye with multiple focal lengths consists of an array of individual lenses with 1000 µm diameter. The simulation results of the designed multifocal bionic compound eye (MBCE) with two focal lengths of 190 mm and 44.4 mm demonstrate excellent two-order focusing abilities. Moving mask exposure technology was used to fabricate the designed MBCE with the corresponding imaging experiments conducted to validate the two-order imaging ability of the fabricated MBCE. Experimental results revealed that the developed structure has potential applications in diverse optical imaging systems such as three-dimensional imaging and real-time detection of unconfined or fluctuating targets.