In order to enhance the collaborative innovation development capability of the Chengdu-Chongqing Twin-City Economic Circle, the evaluation index system of collaborative innovation development ability was constructed from four dimensions of talents, scientific research, industry and innovative ecological environment, and a compound system synergy degree model was used to measure the order degree and synergy degree of collaborative innovation in Chengdu-Chongqing Twin-City Economic Circle during 2016-2018, with basis on the multi-dimensional normal cloud model, the innovation level of each city in the region in 2018 was analyzed. The results show that during the period of 2016-2018, the gap between the development level of collaborative innovation of different regions are gradually widening, and the centripetal force of the overall collaborative development of the region is insufficient, forming a situation that Chengdu and Chongqing are the two cores radiating to the surrounding areas. Based on the above context, it is proposed to recognize the pattern of development, so as to change the "siphon effect" into "driving effect" as well as further optimize the environment for collaborative innovation development, refine the division of labor of the dual-circle industrial chain, solve the problem of the homogeneity competition between the two places to improve the regional collaborative innovation development ability, and promote the high-quality development of the Chengdu-Chongqing Twin-City Economic Circle.