The performance of software cost estimation based on analogy reasoning depends upon the measures that specifying the similarity between software projects. This paper empirically investigates the use of probabilistic-based distance functions to improve the similarity measurement. The probabilistic-based distance functions are considerably more robust, because they collect the implicit correlation between the occurrences of project feature attributes. This information gain enables the constructed estimation model to be more concise and comprehensible. The study compares 6 probabilistic-based distance functions against the commonlyused Euclidian distance. We empirically evaluate the implemented cost estimation model using 5 real-world datasets collected from the PROMISE repository. The result shows a significant improvement in terms of error reduction, that implies an estimation based on probabilistic-based distance functions achieve higher accuracy on average, and the peak performance significantly outperforms the Euclidian distance based on Wilcoxon signed-rank test.