[Objective] Developing condition and early warning research was studied with regard to the security of Shaanxi regional innovation ecosystem in order to provide a theoretical basis for the safe development of Shaanxi regional innovation ecosystem. [Methods] A security measurement index system of the regional innovation ecosystem was constructed based on the niche perspective that included the four dimensions of openness, growth, synergy, and sustainability. The security status of the regional innovation ecosystem in Shaanxi Province from 2011 to 2020 was measured and analyzed by using a niche suitability model. The BP neural network model was used to predict the evolution trend of the regional innovation ecosystem security alarm in Shaanxi Province from 2021 to 2024. [Results] ① The security status of the regional innovation ecosystem in Shaanxi Province showed a steady increase during 2011—2020, indicating that regional innovation development had a good foundation and potential. ② The security status of the regional innovation ecosystem in Shaanxi Province would continue to improve from 2021 to 2024, but the status would still be lower in the north and south and higher in the central part of the province. [Conclusion] The security status of regional innovation ecosystem in Shaanxi Province shows a good trend of evolution, but the innovation ecosystem security of prefecture-level cities has obvious polarization. Therefore, it is still necessary to take relevant measures to further narrow the gap between regions so as to promote the healthy development of Shaanxi regional innovation ecosystem.