Intrusion detection systems examine the computer or network for potential security vulnerabilities. Time series data is real-valued. The nature of the data influences the type of anomaly detection. As a result, network anomalies are operations that deviate from the norm. These anomalies can cause a wide range of device malfunctions, overloads, and network intrusions. As a result of this, the network’s normal operation and services will be disrupted. The paper proposes a new multi-variant time series-based encoder-decoder system for dealing with anomalies in time series data with multiple variables. As a result, to update network weights via backpropagation, a radical loss function is defined. Anomaly scores are used to evaluate performance. The anomaly score, according to the findings, is more stable and traceable, with fewer false positives and negatives. The proposed system’s efficiency is compared to three existing approaches: Multiscaling Convolutional Recurrent Encoder-Decoder, Autoregressive Moving Average, and Long Short Term Medium-Encoder-Decoder. The results show that the proposed technique has the highest precision of 1 for a noise level of 0.2. Thus, it demonstrates greater precision for noise factors of 0.25, 0.3, 0.35, and 0.4, and its effectiveness.