The paper uses data of manufacture of aircrafts and spacecrafts from 1995 to 2013 in China and the method of canonical correlation analysis and granger causality test to research on relationship between innovation inputs and outputs of high-tech industry. The results show that although there is a high correlation between innovation inputs and outputs, the granger causality between them is not clear, which illustrates that positive interactive relationship between them has not been formed. The study can provide theoretical reference for management practice