Physics-informed neural networks (PINNs) have attracted wide attention due to their ability to seamlessly embed the learning process with physical laws and their considerable success in solving forward and inverse differential equation (DE) problems. While most studies are improving the learning process and network architecture of PINNs, less attention has been paid to the modification of the DE system, which may play an important role in addressing some limitations of PINNs. One of the simplest modifications that can be implemented to all DE systems is the variable linear transformation (VLT). Therefore, in this work, we propose the VLT-PINNs that solve the DE systems of the linear-transformed variables instead of the original ones. To clearly illustrate the importance of prior knowledge in determining the VLT parameters, we choose the thin-layer flow problems as our focus. Ten related cases were tested, including the jet flows, wake flows, mixing layers, boundary layers and Kovasznay flows. Based on the principle of normalization and for a better match of the DE system to the preference of NNs, we identify three principles for determining the VLT parameters: magnitude normalization for dependent variables (principle 1), local normalization for independent variables (principle 2), and appropriate scaling for physics-related parameters in inverse problems (principle 3). The VLT-PINNs with the VLT parameters suggested by the proposed principles show excellent performance over all the test cases, while the results are quite poor with the VLT parameters suggested by traditional linear transformations, such as nondimensionalization and global normalization. Comparison studies also show that only under the constraints of the VLT principles can we obtain satisfactory results. Besides, we find tanh is more appropriate as the activation function than sin for thin-layer flow problems, from both posteriori results and priori analyses with physical intuition. We highlight that our VLT method is an attempt to combine the three advantages of accuracy, universality and simplicity, and hope that it can provide new insights into the better integration of prior knowledge, physical intuition and the nature of NNs. The code for this paper is available on https://github.com/CAME-THU/VLT-PINN.