Mating system of animals, as a stable evolutionary strategy, is the result of adaptation to the surroundings as well as their inter-specific environment. About 92% of birds are social monogamous; however, many social monogamous birds have extra-pair paternity (EPP), which shows the difference between social mating system and genetic mating system. Varied tits (Parus varius) are social monogamous, but their genetic mating system is not ascertained. Our research indentified the EPP and determined its ratio. The results showed that 20 of 44 broods (45.45%) had extra-pair nestlings and 38 of 264 nestlings (14.39%) were the result of extra-pair fertilization, which indicated that varied tit was not strictly socially monogamous but with a high level of EPP. Further studies of EPP occurrence in varied tit showed that there was no significant difference between the broods with EPP and without EPP (P=0.504). Comparison of heterozygosity between within pair offspring (WPO) from the broods with EPP and without EPP also showed no significant difference (P=0.118). The same was observed between the extra-pair offspring (EPO) and WPO in the broods with EPP (P=0.206) and additional eight physical indicators of WPO and EPO in broods with EPP (Ps> 0.05). In summary, the emergence of EPP in varied tit was not in favor of the genetic compatibility, which warrants further exploration of other aspects.