By utilizing panel data of provinces in China from 2012 to 2018, this paper measured innovation efficiency of each regional innovation system and the triple helix relationship of the university‐industry‐government system, then, empirically investigated the influence of the triple helix relationship on regional innovation efficiency. It has been found that: (1) the regional innovation efficiency in China increases slightly year by year, the regional differences are obvious, and university–industry bilateral cooperation is the tightest; (2) cooperation between universities and industries is most beneficial to improve regional innovation efficiency, cooperation between universities and governments significantly promotes scale efficiency in the long run, cooperation between industries and governments significantly promotes regional innovation comprehensive efficiency and pure technical efficiency, meanwhile inhibits scale efficiency, coordinated relation among universities, industries, and governments is beneficial to improve regional innovation comprehensive efficiency and scale efficiency. The research results provide useful theoretical support and policy enlightenment for improving regional innovation efficiency.