This study explores the double-edged sword effect of FWAs on employee innovation performance based on the Demand–Resource–Individual Effect (DRIVE) model. A total of 411 valid questionnaires from knowledge-based employees were collected in three stages through a survey of technology-based companies in China. The data were analyzed using SPSS 25.0 and AMOS 22 software, and multi-level linear model analysis was conducted to test the double mediating effect of psychological empowerment and role ambiguity and the moderating effect of role breadth self-efficacy. This study found that, in terms of the job demand path, flexible work arrangements (FWAs) increased employees’ role ambiguity, which in turn decreased their innovation performance; in terms of the job resource path, FWAs increased employees’ psychological empowerment, which in turn increased their innovation performance. From the perspective of individual differences, under the flexible work system, employees with high role breadth self-efficacy can enhance their psychological empowerment and reduce role ambiguity, thus promoting their innovation performance. This study is the first to analyze the “double-edged sword” effect of FWAs on employee innovation performance based on the DRIVE model, which effectively extends the moderating variable of role breadth self-efficacy in the model and helps to understand the impact of different types of FWAs on employee innovation performance. In addition, this study provides a reference for technology-based companies to strengthen their digital capabilities and regulation of FWAs, which is conducive to achieving sustainable business development.