The choice of industry is a primary consideration in corporate venture capital activities, exerting a significant influence on corporate strategic outcomes. Based on the behavioral theory of the firm, this paper examines the impact of negative attainment discrepancy on dual goals—financial and innovative—on the industry selection of corporate venture capital. Furthermore, it incorporates the structural characteristic of investment units, specifically autonomy, into the theoretical framework to delve into its moderating effect. This paper draws the following conclusions from an empirical analysis of investment units controlled by companies listed on Shanghai and Shenzhen Stock Exchanges in China from 2008 to 2018. First, investment units tend to respond to an increase in the negative attainment discrepancy on both financial and innovative goals by increasing cross-industry investments. Second, investment unit autonomy increases their focus on financial performance feedback, reinforcing the positive relationship between negative attainment discrepancy and cross-industry investments. Third, investment unit autonomy reinforces investment managers’ recognition of the higher priority of financial goals over innovative goals. Consequently, when faced with a decline in financial performance, investment units with greater autonomy are more likely to attenuate their response to innovative goals in comparison to those with weaker autonomy. This paper considers both financial and negative goals, extending the behavioral theory of the firm and offering valuable insights for the design of organizational structures in the field of corporate venture capital.