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The Populus euphratica is one of the most important plant species for maintaining desert riparian forests in the lower reaches of Tarim River. Estimation and analysing of trunk volume of trees are crucial to the evaluation of forests biomass and ecosystem services. Although many approaches to estimating trunk volumes have been proposed, they are usually not only labour intensive but also destructive and therefore not feasible for such protected species as P. euphratica. There are two main contributions in this paper: First, we propose a new framework to calculate the volume of tree trunks using point clouds with a deep camera in a Tango smartphone and a Google Play app. Second, a mathematical model is provided for predicting trunk volume based on the relationship between trunk volumes and morphological characteristics. The proposed framework can also deal with irregularly shaped tree trunks. The non-destructive method, which uses an easily accessible and low-cost device, can make a significant contribution to protecting desert riparian forests and is also applicable to other tree species.