From the perspective of global oil and gas exploration trends, deep to ultra-deep gas exploration has emerged as a focal point in the past decade, shaping the future landscape of fossil energy exploration. Specifically, China has undertaken oil and gas exploration ventures reaching depths of 10,000 m, drawing significant attention to the genesis of gas accumulation at such extreme depths. An analysis of crucial geological factors including basin formation, hydrocarbon generation, storage and accumulation reveals that kerogen cracking gas, crude oil cracking gas, and coal cracking gas served as vital gas sources for ultra-deep paraffin gas in highly over-mature oil-bearing basins, establishing a model for the formation, evolution, and accumulation of natural gas. With the continuous expansion of hydrocarbon genesis theory and the increasing global demand for clean energy, hydrogen, as an important link between inorganic and organic hydrocarbon generation theory, and as a promising clean energy, has gradually aroused extensive attention in the academic community. The genetic types of natural hydrogen are mainly generated from inorganic genetic mechanisms, including earth degassing, water-rock interaction, and water radiolysis. The lithology of the reservoir and the sealing property of the cap layer control the accumulation of natural hydrogen, with the salt-rock cap layer beneficial to the large-scale preservation of natural hydrogen reservoir. Helium, as a constituent resource of natural gas, represents the primary target for exploration among deep small molecule gases. Helium within natural gas reservoirs can be categorized into atmospheric, crust-source and mantle-source varieties based on their origins. Helium source rocks exhibit significant disparities in helium generation capacity attributed to variations in rock types, mineral compositions, and ages, resulting in a relatively complex mechanism governing helium reservoir release, migration and accumulation. Typically, helium-rich gas reservoirs lack optimal cap sealing performance, as excessive sealing inhibits the formation of pressure relief conduits, thereby impeding the supply of helium-rich fluid to the reservoir. Through an analysis of genetic types, formation and evolution models, and reservoir preservation mechanisms pertinent to deep alkane gases and small molecule gases, it is revealed that the large-scale pool-forming geologic units and giant hydrocarbon enrichment zones in ultra-deep strata are key and promising prospects for delivering successive discoveries, and the energy significance and development trend of natural hydrogen and helium in the future were pointed out, in order to provide references for promoting the transition from high carbon to low carbon and carbon-free energy in the energy field.