With the rapid development of computer networks and information technology, government departments, financial institutions, and enterprises are increasingly dependent on software, and software security issues have become a focus of attention. In this context, how to effectively evaluate the security of software has become an important issue for research institutions both domestically and internationally. On the basis of exploring software definition, this paper not only analyzes the security and potential threats of software in computer networks, but also introduces Embedded Neural Networks (ENNs) as an evaluation tool, and combines Fuzzy Analytic Hierarchy Process (FAHP) to deeply explore a new method for software security risk assessment. By utilizing the powerful pattern recognition capability of ENNs, software logs, system call sequences, and other data can be classified and analyzed to distinguish between normal and abnormal behavior. This ability is crucial for identifying security incidents such as malicious software and unauthorized access. ENNs are designed with resource constraints in mind, which can reduce energy consumption while ensuring performance. For software systems that require long-term operation, this means higher security and stability. Practice has proven that combining ENNs with FAHP can more scientifically and effectively evaluate software security. This method not only improves the accuracy and efficiency of evaluation, but also provides a more solid theoretical foundation and technical support for software security protection.