The species occurs in forested habitats and roosts in tree cavities (Wilson and Mittermeier 2019). The type series was collected from holes in bamboo stems in Fujian, China, at an elevation of 760 m (Smith and Xie 2008). M. frater has also been found to roost in natural caves and tunnels (Bu et al. 2015). In Taiwan, however, this species inhabits mountainous areas up to over 1,000 m altitude and has been recorded roosting in tree holes in primary, secondary and bamboo forests (Cheng et al. 2017b, Chang 2015), in bat boxes (Chen 2009), in tunnels, but not in caves (Ruedi et al. 2015). Current data suggest that its diet on this island would be mainly composed of lepidopteran (Lu 2013). Overall, very little is known about the ecology of this species and the threats that it might face.

Myotis frater has been recorded in Fujian, Jiangxi, Sichuan, Anhui, Guangdong, and Guizhou provinces in mainland China (Zhang et al. 2000, Smith and Xie 2008, Bu et al. 2015, Lin et al. 2018, Wilson and Mittermeier 2019) and widely distributed across Taiwanese forests from low to moderate elevations (Chang 2015, Ruedi et al. 2015). Five individuals identified as belonging to the M. frater group were also captured in Uttarakhand in the Western Himalayas (India) but their taxonomy remains unsettled (Chakravarty et al. 2020).

The species is not known from any protected areas and there are no species-specific conservation initiatives. Little is known about this species. Monitoring and research concerning its ecological requirements is needed. M. frater is currently listed as Least Concern in Taiwan and is not protected (Cheng et al. 2017a). In China, it is listed as Data Deficient (Jiang et al. 2016).