The existing neural network model in urban land-subsidence prediction is over-reliant on historical subsidence data. It cannot accurately capture or predict the fluctuation in the sequence deformation, while the improper selection of training samples directly affects its final prediction accuracy for large-scale urban land subsidence. In response to the shortcomings of previous urban land-subsidence predictions, a subsidence prediction method based on a neural network algorithm was constructed in this study, from a multi-factorial perspective. Furthermore, the scientific selection of a large range of training samples was controlled using a K-shape clustering algorithm in order to produce this high-precision urban land subsidence prediction method. Specifically, the main urban area of Kunming city was taken as the research object, LiCSBAS technology was adopted to obtain the information on the land-subsidence deformation in the main urban area of Kunming city from 2018–2021, and the relationship between the land subsidence and its influencing factors was revealed through a grey correlation analysis. Hydrogeology, geological structure, fault, groundwater, high-speed railways, and high-rise buildings were selected as the influencing factors. Reliable subsidence training samples were obtained by using the time-series clustering K-shape algorithm. Particle swarm optimization–back propagation (PSO-BP) was constructed from a multi-factorial perspective. Additionally, after the neural network algorithm was employed to predict the urban land subsidence, the fluctuation in the urban land-subsidence sequence deformation was predicted with the LSTM neural network from a multi-factorial perspective. Finally, the large-scale urban land-subsidence prediction was performed. The results demonstrate that the maximum subsidence rate in the main urban area of Kunming reached −30.591 mm⋅a−1 between 2018 and 2021. Moreover, there were four main significant subsidence areas in the whole region, with uneven distribution characteristics along Dianchi: within the range of 200–600 m from large commercial areas and high-rise buildings, within the range of 400–1200 m from the under-construction subway, and within the annual average. The land subsidence tended to occur within the range of 109–117 mm of annual average rainfall. Furthermore, the development of faults destroys the stability of the soil structure and further aggravates the land subsidence. Hydrogeology, geological structure, and groundwater also influence the land subsidence in the main urban area of Kunming. The reliability of the training sample selection can be improved by clustering the subsidence data with the K-shape algorithm, and the constructed multi-factorial PSO-BP method can effectively predict the subsidence rate with a mean squared error (MSE) of 4.820 mm. The prediction accuracy was slightly improved compared to the non-clustered prediction. We used the constructed multi-factorial long short-term memory (LSTM) model to predict the next ten periods of any time-series subsidence data in the three types of cluster data (Cluster 1, Cluster 2, and Cluster 3). The root mean square errors (RMSE) were 0.445, 1.475, and 1.468 mm; the absolute error ranges were 0.007–1.030, 0–3.001, and 0.401–3.679 mm; the errors (mean absolute error, MAE) were 0.319, 1.214, and 1.167 mm, respectively. Their prediction accuracy was significantly improved, and the predictions met the measurement specifications. Overall, the prediction method proposed from the multi-factorial perspective improves large-scale, high-accuracy urban land-subsidence prediction.