This paper presents a pedestrian indoor navigation system based on the multi-sensor fusion and fuzzy logic estimation algorithms. The proposed navigation system is a self-contained dead reckoning navigation that means no other outside signal is demanded. In order to achieve the self-contained capability, a portable and wearable inertial measure unit (IMU) has been developed. Its adopted sensors are the low-cost inertial sensors, accelerometer and gyroscope, based on the micro electro-mechanical system (MEMS). There are two types of the IMU modules, handheld and waist-mounted. The low-cost MEMS sensors suffer from various errors due to the results of manufacturing imperfections and other effects. Therefore, a sensor calibration procedure based on the scalar calibration and the least squares methods has been induced in this study to improve the accuracy of the inertial sensors. With the calibrated data acquired from the inertial sensors, the step length and strength of the pedestrian are estimated by multi-sensor fusion and fuzzy logic estimation algorithms. The developed multi-sensor fusion algorithm provides the amount of the walking steps and the strength of each steps in real-time. Consequently, the estimated walking amount and strength per step are taken into the proposed fuzzy logic estimation algorithm to estimates the step lengths of the user. Since the walking length and direction are both the required information of the dead reckoning navigation, the walking direction is calculated by integrating the angular rate acquired by the gyroscope of the developed IMU module. Both the walking length and direction are calculated on the IMU module and transmit to a smartphone with Bluetooth to perform the dead reckoning navigation which is run on a self-developed APP. Due to the error accumulating of dead reckoning navigation, a particle filter and a pre-loaded map of indoor environment have been applied to the APP of the proposed navigation system to extend its usability. The experiment results of the proposed navigation system demonstrate good navigation performance in indoor environment with the accurate initial location and direction.