Banana Fusarium wilt is one of the most serious diseases that restricts the banana industry. How to achieve efficient, low toxicity, and long-term inhibition of pathogenic fungal spores (Fusarium oxysporum f. sp. cubense, race 4, Foc4) that grow in soil has become a challenge in the field of chemical control of plant diseases in recent years. Based on the special antimicrobial mechanism of guanidine salts, which can effectively inhibit microbes by forming transmembrane stomata on the plasma membrane, we were inspired to introduce hydrophilic guanidine salts to hydrophobic PDMS chains to potentially balance high antimicrobial activity and low environmental toxicity. In this work, a series of novel amphiphilic polysiloxane graft guanidine salts (PDMS-g-GH) were synthesized based on our previous works, i.e., polysiloxane graft primary amine salts (PDMS-g-AH), in which the primary amine salt groups were converted to guanidine salt groups. The molecular weight of the polymer, the grafting density of guanidine salts, the distribution of guanidine salt units on the main chain (random or block), the in vitro antifungal activities and the anti-Foc4 activities in soil, the adsorption characteristics in soil, and the environmental toxicity after soil adsorption were systematically studied. The results confirmed that compared with PDMS-g-AH, PDMS-g-GH showed stronger antifungal activity against Foc4 and long-term antifungal activity against Foc4 in soil, but its environmental toxicity was significantly reduced. These results support the potential application of PDMS-g-GH for the prevention and control of banana Fusarium wilt and other soil-borne fungal diseases.