A deterministic multifunctional architecture design approach for a highly adaptive small satellite system is proposed in this paper. It enables five levels of design customisation of all categories of highly adaptive small satellites; adaptive functional modules implement higher-level customised and reconfigurable mission functions. Each adaptive multifunctional structural unit (AMSU) supports the subsystem functions as a ‘structural and functional block’ and comes either as a baseline or hybrid. Associated functional sub subsystem components are contained in each AMSU. This removes the conventional structural and functional subsystem boundaries. A meteorology spacecraft mission using a highly adaptive nanosatellite reveals, besides more advanced mission capabilities, 0.6 kg and 1 W mass- and power-savings respectively over a conventional nanosatellite system implementation. This novelty results in adaptive, reconfigurable and multifunctional architectures with economies of scale, timely launch, system-level reliability, flexible integration and test options, cost-effective mass production, post-mission reapplication and optimal performance at the desired mission objectives.