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Quantifying and comparing sustainability indicators are essential to improve the sustainability of smallholder rice cropping systems. The sustainability of rice production systems can be measured based on economic, environmental, social, and institutional indicators. In this paper, we restrict our assessment to economic and environmental indicators. During 2012–2015, farmers were interviewed from 847 households from intensively irrigated rice production regions in Vietnam, Thailand, Indonesia, Myanmar, Sri Lanka, and China. We assessed the sustainability of their farming practices using economic and environmental indicators, i.e., eight of the 12 performance indicators (PIs), as defined by the Sustainable Rice Platform (SRP). Across the six sites, there was a yield gap of 24–42% and a profit gap of 36–82% between the 10% highest-performing farms (mean of top decile) and the mean-performing farms. In addition, there was a labor productivity gap of 12–32%, a nitrogen use efficiency (NUE) gap of 11–20%, a phosphorus use efficiency (PUE) gap of 1–29%, and a water productivity gap of 12–42%. Deliberate modification of conventional practices, including not flooding the field for >30 days before rice planting, incorporating pre-rice crop residue >30 days before planting, and adoption of mid-season drainage or alternate wetting and drying irrigation rather than continuous flood irrigation during the rice growing period, could substantially reduce the greenhouse gas (GHG) emission in irrigated rice fields without yield penalty. There is an urgent need to adopt improved management strategies for nitrogen (N), phosphorus (P), potassium (K) fertilizer, irrigation water-use efficiency, as well as for decreasing pesticide use frequency, without sacrificing profitability and yield. We identified the following priority interventions for each site: a) increasing fertilizer use and adopting higher-yielding varieties in Bago, Myanmar; b) reducing pesticide application rates in Can Tho, Vietnam; c) reducing fertilizer use in Guangdong, China; d) reducing nitrogen and labor use in Yogyakarta, Indonesia; e) reducing fertilizer and water use in Polonnaruwa, Sri Lanka and; f) reducing fertilizer use in Nakhon Sawan, Thailand. Additional uses of the PI analysis clearly demonstrated that rice yield and profit gaps can sustainably be closed by increasing efficiencies that will also lead to reduced environmental footprint.