Background: Three-dimensional facial soft tissue landmark prediction is an important tool in dentistry, for which several methods have been developed in recent years, including a deep learning algorithm which relies on converting 3D models into 2D maps, which results in the loss of information and precision. Methods: This study proposes a neural network architecture capable of directly predicting landmarks from a 3D facial soft tissue model. Firstly, the range of each organ is obtained by an object detection network. Secondly, the prediction networks obtain landmarks from the 3D models of different organs. Results: The mean error of this method in local experiments is $2.62\pm 2.39$, which is lower than that in other machine learning algorithms or geometric information algorithms. Additionally, over 72% of the mean error of test data falls within $\pm 2.5$ mm, and 100% falls within 3 mm. Moreover, this method can predict 32 landmarks, which is higher than any other machine learning-based algorithm. Conclusions: According to the results, the proposed method can precisely predict a large number of 3D facial soft tissue landmarks, which gives the feasibility of directly using 3D models for prediction.