We are currently in surroundings with ubiquitous software-embedded products, while there is less understanding on innovations of the invisible embedded software (ESW). Because of its significant role in automobiles and big market share in the Japanese ESW sector, automotive software (ASW) is selected as the case for our research on heterogeneity and typology of product innovation in ESW. Based on the embedded nature of ASW, the role of Japanese automobiles in the USA and the advantage of using patenting in large third countries as a good proxy measure for national innovation activities, we employ ASW-related patents in the USPTO patent database as an indicator of ASW product innovation. Through analysing the heterogeneities of product innovation in terms of function and actors’ innovation activities over the period 1981–2010 by classifying ASW functions into fields of power train control, battery and electric power control, safety control, body control and information communication and telecommunication system, we extract the product innovation typology of ESW and conclude that the heterogeneous requirements for real-time operation and accumulation of specific knowledge are the main reasons of heterogeneity of product innovation in ESW. These results imply different R&D strategies and innovation trajectories.