The effect of the main characteristics of low molecular weight chitosan obtained via enzymatic and chemical hydrolysis with a molecular mass (MM) of 2–100 kDa, a deacetylation degree (DD) of 60–98%, and a polydispersity (Mw/Mn) of 1.9–2.7 on the growth of Botrytis cinerea has been studied. The greatest inhibitory effect on the fungal germination process (a conidia germination index of less than 50%) was provided by chitosan samples with an MM of 2–13 kDa, a DD of 85–98%, and a polydispersity of 2–2.5. Among the most effective was chitosan with an MM of 13 kDa and a deacetylation degree 98%, which had a significant inhibitory effect on the growth of the fungal mycelium at concentration 0.938 mg/mL. This sample of chitosan and its complex with copper ions (75 ppm) significantly suppressed fungal metabolic activity (up to 20 and 10%, respectively), which indicates their high potential as antifungal agents for the development of fungicides.