Electrocatalytic water splitting has appeared to be a sustainable green technology for hydrogen and oxygen production, and noble metal-based electrocatalysts, like Pt for hydrogen evolution reaction (HER) and RuO2/IrO2 for oxygen evolution reaction (OER) have been proved to be state-of-the-art in water electrolyzers. However, high cost and scarcity of noble metals hinder large-scale applications of these electrocatalysts in practical commercial water electrolyzers. As an alternative, transition metal based electrocatalysts have attracted great attention because of the exciting catalytic performance, cost-effectiveness and abundant availability. However, their long-term stability in water splitting devices is unsatisfactory because of agglomeration and dissolution in the harsh operating environment. A possible solution to this issue is encapsulating transition metal (TM) based materials in stable and highly conductive carbon nanomaterials (CNMs) to make a hybrid of TM/CNMs, and the performance of TM/CNMs could be further enhanced by heteroatom (N-, B-, and dual N,B-) doping to carbon network in CNMs to break the carbon electroneutrality due to the different electronegativity, modulate the electronic structure to facilitate the adsorption of reaction intermediates, and promotion of efficient electron transfer to enhance the number of catalytically active sites for water splitting operation. In this review article, the recent progress of TM-based materials hybridizing with CNMs, N-CNMs, B-CNMs, and N,B-CNMs as electrocatalysts towards HER, OER as well as overall water splitting have been summarized, and the challenges and future prospects are also discussed.