Abstract: Under the condition of deep digitization, how embeddedness of digital technology in breakthrough innovation eliminate industry barriers and the uncertainty of technological innovation and how latecomer take advantage of the "window of opportunity" of digital breakthrough innovation are urgent issues to be solved at present. Based on systematically analyzing new connotation and new characteristics of breakthrough innovation under the condition of deep digitalization, the mechanism and innovation paths of how deep digitization promoting breakthrough innovation under the scenario of late-developing country were expounded theoretically. Some solutions to overcome multiple barriers at organizational, industrial and national level by using digital means were proposed. Furthermore, challenges and countermeasures for future breakthrough innovation were came up to provide references for expanding the theoretical system of breakthrough innovation under the condition of deep digitization and exploring new opportunities of breakthrough innovation in latecomers represented by China.