Arbuscular mycorrhizal fungi (AMF) function mostly depends on their colonization to roots. However, it has not been systematically clear how arbuscular mycorrhiza (AM) formation is affected by organic contaminants. In this study, a meta-analysis was performed to estimate the effects of three groups of organic contaminants (polycyclic aromatic hydrocarbons (PAHs), crude oil, and pesticide) in soil on mycorrhizal colonization rates (MCRs) from various moderators, such as AMF (genus, species, and inoculation mode), contaminant (level, type, and source), and experimental conditions (plant type, duration, and soil sterilization). Our results showed that all MCRs (total, vesicular, arbuscular and hyphal) significantly decreased under the stresses of three contaminants. Generally, pesticide caused larger decrease in all MCRs than PAHs and crude soil except for vesicular MCRs. Mixed AMF showed larger decrease in the total and vesicular MCRs than single AM fungus, but contrary trends in the arbuscular and hyphal MCRs. Moreover, man-made contaminant seemed to produce larger negative effects on the total, vesicular, and arbuscular MCRs than industry contaminant. The inhibitive effects of three contaminants on the total and vesicular MCRs increased with increasing experimental duration, and were larger in the non-sterilized soil than in the sterilized soil. Hyphal and spore growth were also inhibited by three contaminants in most cases. Hyphal length and spore number of single AM fungus were lower than those of mixed AMF, and pesticide produced larger inhibition on the hyphal length and spore number than PAHs and crude oil. Similar trend was found in the non-sterilized soil relative to the sterilized soil. This study indicated that AM formation and AM structure were negatively affected by three organic contaminants, whereas the inhibitive degrees varied with AMF, organic contaminant and experimental conditions.