A new approach is proposed to detect micro and small damages in multi-span bridges constructed with variable sections by combining modal strain energy and spectral finite element through the use of machine learning techniques. The traditional finite element methods are inefficient in detecting and estimating structures' micro-damages. Therefore, wave propagation-based methods must be applied. Micro-damages can be modeled through the spectral finite element method, widely adopted in wave propagation simulation. Among the frequency-based methods used in damage identification, the modal strain energy is more sensitive, especially in complicated structures. However, this method is difficult to apply to steel girders with variable sections and different support conditions. By combining the modal strain energy and the spectral finite element and applying the support vector regression method, the location and severity of damage in steel girders could be accurately identified to overcome the difficulties of detection in complicated elements. To improve the ability of the support vector regression method, in the damage severity estimation, it was combined with feature selection. To evaluate the proposed method's ability, first, an element of the beam- type, with the characteristics of a spectral finite element, is defined in the OpenSees software. To assess the accuracy of the defined element in detecting micro-damages, a tested numerical model was adopted to measure the accuracy of the provided element. Next, to detect small damages, the model of the steel girder bridge with the defined element was prepared, and the modal properties of the structure were extracted. Due to the change in cross-section along each girder, the modified modal strain energy-based damage index (β) equation was used in the subject model. By applying the damages of different severities in steel girders in single and multiple damage scenarios, the modified damage index β was calculated. With the damage indexes calculated in the different scenarios and applying the machine learning method, the severity of damage was estimated. The obtained results indicate that this proposed method is accurate and satisfactory for detecting and estimating micro and small damages with high accuracy in bridges with variable section girders.