In engineering practice, the amount of measured data is often scarce and limited, posing a challenge in uncertainty quantification (UQ) and propagation. Data-driven polynomial chaos (DDPC) is an effective way to tackle this challenge. However, the DDPC method faces problems from the lack of robustness and convergence difficulty. In this paper, a preconditioner-based data-driven polynomial chaos (PDDPC) method is developed to deal with UQ problems with scarce measured data. Two numerical experiments are used to validate the computational robustness, convergence property, and application potential in case of scarce data. Then, the PDDPC is first applied to evaluate the uncertain impacts of real leading edge (LE) errors on the aerodynamic performance of a two-dimensional compressor blade. Results show that the overall performance of compressor blade is degraded and there is a large performance dispersion at off-design incidence conditions. The actual blade performance has a high probability of deviating from the nominal performance. Under the influence of uncertain LE geometry, the probability distributions of the total pressure loss coefficient and static pressure ratio have obvious skewness characteristics. Compared with the PDDPC method, the UQ results obtained by the fitted Gaussian and Beta probability distributions seriously underestimate the performance dispersion of compressor blade. The mechanism analysis illustrates that the large flow variation around the leading edge is the main reason for the overall performance degradation and the fluctuations of the entire flow field.