Micellar affinity gradient focusing (MAGF) is a microfluidic counterflow gradient focusing technique that combines the favorable features of MEKC and temperature gradient focusing. MAGF separates analytes on the basis of a combination of electrophoretic mobility and partitioning with the micellar phase. A temperature gradient is produced along the separation channel containing an analyte/micellar system to create a gradient in interaction strength (retention factor) between the analytes and micelles. Combined with a bulk counterflow, species concentrate at a unique point where their total velocity sums to zero. MAGF can be used in scanning mode by varying the bulk flow so that a large number of analytes can be sequentially focused and passed by a single detection point. In this work, we develop a bilinear temperature gradient along the separation channel that improves separation performance over the conventional linear designs. The temperature profile along the channel consists of a very sharp gradient used to preconcentrate the sample followed by a shallow gradient that increases resolution. We fabricated a hybrid PDMS/glass microfluidic chip with integrated micro heaters that generate the bilinear profile. Performance is characterized by separating several different samples including fluorescent dyes using SDS surfactant and pI markers using both SDS and poly-SUS surfactants as the micellar phase. The new design shows a nearly two times improvement in peak capacity and resolution in comparison to the standard linear temperature gradient.