Barrowby and Allington were judged joint winners in the larger village category while Irnham took the top spot in the smaller villages/hamlets category.
Caythorpe and Thurlby were second and third respectively as larger villages, and Stoke Rochford and Greatford were second and third as smaller villages/hamlets.
Each of the winners will receive £400, with £300 going to second place villages and £200 to those in third.
Cllr Dr Peter Moseley, SKDC's Cabinet Member for Commercial and Operations, said: "Choosing our winners has been extremely challenging this year because the standards were so high.
"In the end the fairest thing to do was to split the larger village honours between Barrowby and Allington. Overall, however, what was very obvious from the front-runners was the community support in those villages.
"I am delighted to see how attractive the district is looking. Alongside that we now have detailed reports on the state of our villages to help us focus the work of our Big Clean team to clean up any problem areas and help improve communities."
More than 100 villages and hamlets were visited as part of this year's competition. Council staff were joined by representatives from the Lincolnshire Gardens Trust and the Royal Horticultural Society to look at the condition of village facilities and evidence of community pride.
They judged each village on a range of criteria, including: the condition of roadside seats, litter bins, paths and information signs; the condition of front gardens; community pride and ownership, floral features, condition of focal points and village hall/community centres.