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Pimavanserin is an approved selective 5-HT_2A receptor inverse agonist for treating Parkinson’s disease psychosis. However, few studies on its metabolism in vitro have been investigated. In this research, eight strains of fungi are used to study the pimavanserin metabolism profiles in vitro and six of them demonstrated positive transformation results. Factors influencing the transformation rate, like substrate concentration, culture time, initial media pH value, culture temperature, and shaking speed, were evaluated and optimized. <i>Cunninghamella blakesleeana</i> AS3.970 provided the best transformation rate of 30.31%, and 10 unreported metabolites were screened by LC-MS/MS. Among these metabolites, M1 is the major one and identified as 1-(4-fluorobenzyl)-3-(4-(2-hydroxy-2-methylpropoxy)benzyl)-1-(1-methylpiperidin-4-yl)urea, which is a hydroxylation product of the pimavanserin. A preliminary molecular docking simulation was performed, which indicated that M1 exhibits similar binding properties with pimavanserin and may become a potential candidate for Parkinson’s disease treatment.