Fusarium wilt is a soil-borne disease that leads to wilting, yellowing, and sometimes death of various plant species. This article examines the correlations between physicochemical properties and molecular invariants of the chemical structures of molecular biocontrol agents used to mitigate Fusarium wilt, a plant disease. The study considers effective agents like fungicides (thiophanate-methyl, azoxystrobin, trifloxystrobin, fludioxonil, and metalaxyl), soil fumigants (chloropicrin, metam sodium, and 1,3-dichloropropene), and molecular biocontrol agents (methionine and adenosine). This is the first review of QSPR studies on plant diseases in the literature. For the chemical structures of these molecular biocontrol agents, we have calculated M-polynomials of various molecular invariants, including the Zagreb-type indices, atom-bond connectivity index, harmonic index, Sombor index, forgotten index, and symmetric division degree index. The relationships identified through regression analysis provide insights into their effectiveness and optimization. Our findings highlight the best regression coefficients, which have the lowest RMSE and the maximum F-statistics values for significant correlations. Using these regression coefficients, we can predict the behavior of bioagents.