This study addresses the need to reduce the risk of clogging when preparing samples for cell concentration, i.e., the CaSki Cell-lines (epidermoid cervical carcinoma cells). Aiming to develop a non-clogging microconcentrator, we proposed a new counter-flow concentration unit characterized by the directions of penetrating flows being at an obtuse angle to the main flow, due to employment of streamlined turbine blade-like micropillars. Based on the optimization results of the counter-flow unit profile, a fractal arrangement for the counter-flow concentration unit was developed. A counter-flow microconcentrator chip was then designed and fabricated, with both the processing layer and collecting layer arranged in terms of the honeycomb structure. Visualized experiments using CaSki cell samples on the microconcentrator chip demonstrated that no cell-clogging phenomena occurred during the test and that no cells were found in the final filtrate. The test results show an excellent concentration performance for the microconcentrator chip, while a concentrating ratio of >4 with the flow rate being below 1.0 ml/min. As only geometrical structure is employed in the passive device, the counter-flow microconcentrator can be easily integrated into advanced microfluidic systems. Owing to the merit of non-clogging and continuous processing ability, the counter-flow microconcentrator is not only suitable for the sample preparation within biomedical field, but also applicable in water-particle separation.