The Japanese Quasi-Zenith Satellite System (QZSS) has been developed as a GPS (Global Positioning System) complementary system to improve positioning accuracy in the Asia-Pacific region. However, the accuracies of ultra-rapid predicted clocks are not high enough for real-time applications, so it is still a challenge problem. This paper focuses on the clock predictions of the new QZSS constellation. Based on the QZSS clock periodic characteristics, an improved clock prediction method combining the spectrum analysis model (SAM) and extreme learning machine (ELM) is proposed with abbreviation as iELM. The key parameters of iELM are selected carefully including the number of hidden layer nodes and activation function. Further, the input length of the iELM network is optimized and discussed thoroughly. For the purpose of assessing the performance of the proposed algorithm, the clock prediction accuracies are compared among GBU-P (the ultra-rapid predicted orbits/clocks provided by GFZ (Deutsches GeoForschungsZentrum)), SAM and iELM methods. It is demonstrated that iELM keeps in a high level of accuracy below 1.0ns with the predicted time increasing from 0 to 18h, and a little larger during the next six hours. And the QZO (Quasi-Zenith Orbit) satellites perform better than GEO (Geostationary Earth Orbit) satellite. Furthermore, precise point positioning (PPP) for both static and kinematic modes are experimentally studied for 13 IGS (International GNSS (Global Navigation Satellite System) Service) MGEX (Multi-GNSS Experiment) stations in the longitude range between 100°E and 180°E. In the static PPP mode, the iELM method is verified to be effective for the GPS/QZSS constellation as positioning accuracy is improved by 28.3%, 57.7% and 47.4% on average in the east, north and up component with respect to GPS/QZSS GBU-P results. Nearly 70.0% stations achieve sub-decimeter accuracy in the vertical component. As for the kinematic PPP, the iELM method based on GPS/QZSS observations performs much better than the others for shorter convergence time and better positioning accuracy. Compared with GPS/QZSS GBU-P, iELM takes at most a half time to get convergence, and the accuracy is enhanced by 27.6%, 23.7% and 13.9% on average in the east, north and up direction respectively.