Hypokinetic dysarthria, which is associated with Parkinson’s disease (PD), affects several speech dimensions, including phonation. Although the scientific community has dealt with a quantitative analysis of phonation in PD patients, a complex research revealing probable relations between phonatory features and progress of PD is missing. Therefore, the aim of this study is to explore these relations and model them mathematically to be able to estimate progress of PD during a two-year follow-up. We enrolled 51 PD patients who were assessed by three commonly used clinical scales. In addition, we quantified eight possible phonatory disorders in five vowels. To identify the relationship between baseline phonatory features and changes in clinical scores, we performed a partial correlation analysis. Finally, we trained XGBoost models to predict the changes in clinical scores during a two-year follow-up. For two years, the patients’ voices became more aperiodic with increased microperturbations of frequency and amplitude. Next, the XGBoost models were able to predict changes in clinical scores with an error in range 11–26%. Although we identified some significant correlations between changes in phonatory features and clinical scores, they are less interpretable. This study suggests that it is possible to predict the progress of PD based on the acoustic analysis of phonation. Moreover, it recommends utilizing the sustained vowel /i/ instead of /a/.