Selecting a sustainable cross-country natural gas pipeline project portfolio plays a vital role in enhancing energy security and national self-reliance. The interdependencies between projects augment the complexity of project portfolio selection. Hence, the selection must be done with sustainable strategic alignment and adjustment of ongoing projects to determine the most suitable project portfolio. This is while they have barely been addressed simultaneously in the literature. The aim of the present study is to fill in the mentioned gap by establishing an integrated framework incorporating the organization strategies, project interdependencies, and ongoing projects in the project portfolio selection problem. This presented framework uses network mapping to visualize project interdependencies and improve the quality of the resulting decision. The decision-aid approach of Measuring Attractiveness by a Categorical Based Evaluation Technique (MACBETH) was employed to tackle multi-criteria value measurement in project portfolio selection. Applicability and validity of the proposed framework were tested using the case study of the Iranian Gas Engineering and Development Company (IGEDC). The pipeline project portfolios were analyzed on the basis of experts’ opinions with regard to technical and sustainability strategic criteria (economic, environmental, and social pillars).