This paper delves into the nuanced dynamics influencing the outcomes of risk assessment (RA) in scientific research projects (SRPs), employing the Naive Bayes algorithm. The methodology involves the selection of diverse SRPs cases, gathering data encompassing project scale, budget investment, team experience, and other pertinent factors. The paper advances the application of the Naive Bayes algorithm by introducing enhancements, specifically integrating the Tree-augmented Naive Bayes (TANB) model. This augmentation serves to estimate risk probabilities for different research projects, shedding light on the intricate interplay and contributions of various factors to the RA process. The findings underscore the efficacy of the TANB algorithm, demonstrating commendable accuracy (average accuracy 89.2%) in RA for SRPs. Notably, budget investment (regression coefficient: 0.68, P < 0.05) and team experience (regression coefficient: 0.51, P < 0.05) emerge as significant determinants obviously influencing RA outcomes. Conversely, the impact of project size (regression coefficient: 0.31, P < 0.05) is relatively modest. This paper furnishes a concrete reference framework for project managers, facilitating informed decision-making in SRPs. By comprehensively analyzing the influence of various factors on RA, the paper not only contributes empirical insights to project decision-making but also elucidates the intricate relationships between different factors. The research advocates for heightened attention to budget investment and team experience when formulating risk management strategies. This strategic focus is posited to enhance the precision of RAs and the scientific foundation of decision-making processes.