Thesis writing is one of the most demanding tasks Indonesian EFL students face, requiring them to coordinate linguistic accuracy, methodological reasoning, and disciplinary argumentation in a foreign language. While prior research has documented individual difficulties in Indonesian EFL thesis writing, few studies have examined how these difficulties vary across undergraduate, master's, and doctoral levels, or how linguistic, methodological, socio-cultural, institutional, and technological barriers interact within a single writing process. This study addresses that gap using a sequential explanatory mixed-methods design, combining a structured survey of 23 Indonesian EFL students (13 undergraduate, 4 master's, 5 doctoral, and 1 fresh graduate) with semi-structured interviews with six purposively selected participants across the three academic levels. Survey results show that referencing and citation management was rated as the most difficult stage of thesis writing (M = 3.17), ahead of topic selection and academic English writing, while cross-level comparison reveals that master's respondents reported the greatest difficulty with grammar and vocabulary, whereas doctoral respondents reported the greatest difficulty with topic selection and referencing. Interview data explain this divergence: undergraduate difficulties centered on idea development and citation mechanics, master's difficulties on renewed methodological and linguistic demands despite prior training, and doctoral difficulties on interdisciplinary theoretical positioning, argument coherence, and sustained self-regulation under institutional and supervisory pressure. Advisor feedback emerged as the most valued support mechanism, though its perceived quality varied considerably across participants. The findings support a developmental, level-sensitive model of academic-writing support that integrates language instruction, research methodology, feedback quality, self-regulation, and responsible use of digital and AI-assisted writing tools, rather than a uniform, one-size-fits-all approach to thesis-writing instruction.