With the development of IoT and artificial intelligence, location-based services are getting more and more attention. For solving the current problem that indoor positioning error is large and generalization is poor, this paper proposes a Model Stacking Algorithm for Indoor Positioning System using WiFi fingerprinting. Firstly, we adopt a model stacking method based on Bayesian optimization to predict the location of indoor targets to improve indoor localization accuracy and model generalization. Secondly, Taking the predicted position based on model stacking as the observation value of particle filter, collaborative particle filter localization based on model stacking algorithm is realized. The experimental results show that the algorithm can control the position error within 2m, which is superior to KNN, GBDT, Xgboost, LightGBM, RF. The location accuracy of the fusion particle filter algorithm is improved by 31%, and the predicted trajectory is close to the real trajectory. The algorithm can also adapt to the application scenarios with fewer wireless access points.