In satellite layout design, heat source layout optimization (HSLO) is an effective technique to decrease the maximum temperature and improve the heat management of the whole system. Recently, deep learning surrogate assisted HSLO has been proposed, which learns the mapping from layout to its corresponding temperature field, so as to substitute the simulation during optimization to decrease the computational cost largely. However, it faces two main challenges: 1) the neural network surrogate for the certain task is often manually designed to be complex and requires rich debugging experience, which is challenging for the designers in the engineering field; 2) existing algorithms for HSLO could only obtain a near optimal solution in single optimization and are easily trapped in local optimum. To address the first challenge, considering reducing the total parameter numbers and ensuring the similar accuracy as well as, a neural architecture search (NAS) method combined with Feature Pyramid Network (FPN) framework is developed to realize the purpose of automatically searching for a small deep learning surrogate model for HSLO. To address the second challenge, a multimodal neighborhood search based layout optimization algorithm (MNSLO) is proposed, which could obtain more and better approximate optimal design schemes simultaneously in single optimization. Finally, two typical two-dimensional heat conduction optimization problems are utilized to demonstrate the effectiveness of the proposed method. With the similar accuracy, NAS finds models with 80% fewer parameters, 64% fewer FLOPs and 36% faster inference time than the original FPN. Besides, with the assistance of deep learning surrogate by automatic search, MNSLO could achieve multiple near optimal design schemes simultaneously to provide more design diversities for designers.