The Exoplanet Characterisation Observatory (EChO) is a space mission dedicated to undertaking spectroscopy of transiting exoplanets over the widest wavelength range possible. It is based around a highly stable space platform with a 1.2 m class telescope. The mission is currently being studied by ESA in the context of a medium class mission within the Cosmic Vision programme for launch post 2020. The payload instrument is required to provide simultaneous coverage from the visible to the mid-infrared and must be highly stable and effectively operate as a single instrument. This paper presents the architectural design for the highly interlinked mechanical and thermal aspects of our instrument design. The instrument will be passively cooled to approximately 40K along with the telescope in order to maintain the necessary sensitivity and photometric stability out to mid-infrared wavelengths. Furthermore other temperature stages will be required within the instrument, some of which will implement active temperature control to achieve the necessary thermal stability. We discuss the major design drivers of this complex system such as the need for multiple detector system temperatures of approximately 160K, 40K and 7K all operating within the same instrument. The sizing cases for the cryogenic system will be discussed and the options for providing the cooling of detectors to approximately 7K will be examined. We discuss the trade-offs that we are undertaking to produce a technically feasible payload design which will enable EChO’s exciting science.