During the research and development of multiphase flowmeters, errors are often used to evaluate the advantages and disadvantages of different devices and algorithms, whilst an in-depth uncertainty analysis is seldom carried out. However, limited information is sometimes revealed from the errors, especially when the test data are scant, and this makes an in-depth comparison of different algorithms impossible. In response to this problem, three combinations of sensing methods are implemented, which are the “capacitance and cross-correlation”, the “cross-correlation and differential pressure” and the “differential pressure and capacitance” respectively. The analytical expressions of the gas/liquid flowrate and the associated standard uncertainty have been derived, and Monte Carlo simulations are carried out to determine the desired probability density function. The results obtained through these two approaches are basically the same. Thereafter, the sources of uncertainty for each combination are traced and their respective variations with flowrates are analyzed. Further, the relationship between errors and uncertainty is studied, which demonstrates that the two uncertainty analysis approaches can be a powerful tool for error prediction. Finally, a novel multi-sensor fusion algorithm based on the uncertainty analysis is proposed. This algorithm can minimize the standard uncertainty over the whole flowrate range and thus reduces the measurement error.