The introduction of data-driven inertial navigation provides new opportunities that the pedestrian dead reckoning could not well provide for constraining inertial system error drift on smartphones, and has been considered as another promising approach to meet the requirement of location-based services. However, indoor localization systems based on a single technology still have their limitations, such as the drift of inertial navigation and the received signal strength fluctuation of Bluetooth, making them unable to provide reliable positioning. To exploit the complementary strengths of each technology, this paper proposes a feasible fusion framework by utilizing a particle filter to integrate data-driven inertial navigation with localization based on Bluetooth Low Energy (BLE). For data-driven inertial navigation, under the premise of using the deep neural network with great potential in model-free generalization to regress pedestrian motion characteristics, we effectively combined the method of using gravity to stabilize inertial measurement units data to make the network more robust. Experimental results show that in the test of different smartphone usages, the proposed data-driven inertial navigation and BLE-based localization technology have good results in modeling user’s movement and positioning respectively. And due to this, the proposed fusion algorithm has almost unaffected by the usages of smartphones. Compared with BLE-based localization that achieved a good mean positional error (MPE) of 1.76m, for the four usages of texting, swinging, calling and pocket, the proposed fusion algorithm reduced the MPE by 32.35%, 20.51%, 20.74%, and 45.37%, respectively, and can further improve localization accuracy on the basis of existing fusion method.