Cryogenic mixed refrigerant cycles (CMRCs) offer a cost-efficient method for cooling in the temperature range between 80 and 200 K. The performance of CMRCs is considerably influenced by the entropy production in the main heat exchanger. Therefore, high process efficiencies require small temperature gradients among the fluid streams as well as small pressure drops and limited axial heat conduction. This is best achieved with micro-structured heat exchangers, where large volumetric heat transfer areas can be realized. The zeotropic refrigerant mixtures applied in CMRCs render the heat exchanger design process challenging, since inconstant fluid properties, two-phase heat transfer and pressure drop have to be considered simultaneously. Furthermore, only few data on the convective boiling/condensation kinetics of zeotropic mixtures is available in literature. This contribution presents the design process of a micro-structured heat exchanger with a newly developed numerical model. The governing equations and the solution strategy are presented, followed by the final design and first experimental results.